Child pages
  • Bioinformatics software listing
Skip to end of metadata
Go to start of metadata

The following software packages are installed on the RCAC compute clusters.

To access them, use the module command as described in the RCAC user manual 

First, you need to configure it by entering the following commands:

module load bioinfo

After that, you can use the module load command to access the software you want to use

For instance, module load blast will enable the NCBI BLAST software.

Contact the Bioinformatics Core Director if you want additional software installed.

  1. ABySS
  2. module name: abyss
    version 2.0.2-maxk64
    Other versions: 1.3.2, 1.3.6-conte-maxk64, 1.3.6-gcc-maxk128, 1.3.6-gcc-maxk256, 1.3.6-gcc-maxk64, 1.3.6-gcc-maxk96, 1.3.6-intel-maxk128, 1.3.6-intel-maxk256, 1.3.6-intel-maxk64, 1.3.6-intel-maxk96, 1.3.7-gcc-maxk128, 1.3.7-gcc-maxk256, 1.3.7-gcc-maxk64, 1.3.7-gcc-maxk64-nosparsehash, 1.3.7-gcc-maxk96, 1.5.0-gcc-maxk128, 1.5.0-gcc-maxk256, 1.5.0-gcc-maxk64, 1.5.0-gcc-maxk64-nosparsehash, 1.5.0-gcc-maxk96, 1.5.1-gcc-maxk128, 1.5.1-gcc-maxk256, 1.5.1-gcc-maxk64, 1.5.1-gcc-maxk96, 1.5.2-gcc-maxk128, 1.5.2-gcc-maxk256, 1.5.2-gcc-maxk64, 1.5.2-gcc-maxk96, 1.5.2-maxk128, 1.5.2-maxk256, 1.5.2-maxk64, 1.5.2-maxk96, 1.9.0-intel-maxk64, 1.9.0-intel-nompi-maxk64, 1.9.0-maxk128, 1.9.0-maxk256, 1.9.0-maxk64, 1.9.0-maxk64-nosparsehash, 1.9.0-maxk96, 1.9.0-nompi-maxk64, 2.0.2-maxk128, 2.0.2-maxk256, 2.0.2-maxk96, max128, max256, max96, maxk64

    Assembly By Short Sequences
    http://www.bcgsc.ca/platform/bioinfo/software/abyss
    Info in /group/bioinfo/apps/apps/abyss-2.0.2-maxk64/share/doc/abyss
    Use "man ABYSS" (also man pages for abyss-pe and abyss-tofastq)
    Info: http://www.bcgsc.ca/downloads/abyss/doc/
    This version is compiled with support for maximum k-mer size of 64
    Uses gcc compiler suite

    Depends on gcc
    Depends on Boost
    Depends on openmpi

  3. ABySS samtobreak
  4. module name: abyss-samtobreak
    version 1.3.7

    Calculate contig and scaffold contiguity and correctness metrics
    Part of ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
    Info probably in /group/bioinfo/apps/apps/abyss-samtobreak-1.3.7/share/doc/abyss
    Info: http://www.bcgsc.ca/downloads/abyss/doc/

  5. agrep
  6. module name: agrep
    version 2.04

    Fast text searching allowing errors
    ftp://ftp.cs.arizona.edu/agrep
    Info: /group/bioinfo/apps/apps/agrep-2.04/README
    Info: man agrep

    Depends on gcc

  7. ALLPATHS-LG
  8. module name: allpathslg
    version 52488
    Other versions: 40969, 41634, 42667, 48686, 52415

    Whole genome shotgun assembler
    http://www.broadinstitute.org/software/allpaths-lg/blog/
    ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/
    Manual at ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/AllPaths-LG_Manual.pdf
    Manual at /group/bioinfo/apps/apps/allpathslg-52488/share/doc/allpathslg/AllPaths-LG_Manual.pdf

    Depends on gcc
    Depends on gmp
    Depends on picard-tools

  9. Amalgamated likelihood estimation (ALE)
  10. module name: ALE
    version 2017-09-21

    Probabilistically explore reconciled gene trees
    https://github.com/ssolo/ALE

    Depends on Boost/1.65.1
    Depends on BppSuite

  11. AMOS
  12. module name: amos
    version 3.1.0
    Other versions: 3.0.0

    AMOS (A Modular, Open-Source whole genome assembler)
    http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
    Info in /group/bioinfo/apps/apps/amos-3.1.0/share/doc/

    Depends on gcc
    Depends on perl
    Depends on blat
    Depends on MUMmer
    Depends on cross_match
    Depends on lucy
    Depends on rhel5libs

  13. AmpliconNoise
  14. module name: rdp_classifier
    version 2.4
    Other versions: 2.12, 2.2

    Bayesian classifier
    http://sourceforge.net/projects/rdp-classifier/
    http://rdp.cme.msu.edu/
    Info: /group/bioinfo/apps/apps/rdp_classifier_2.4/README
    Docs: /group/bioinfo/apps/apps/rdp_classifier_2.4/docs/

    Depends on java

  15. ANNOVAR
  16. module name: annovar
    version 2015-03-22

    Functionally annotate genetic variants detected from diverse genomes
    http://annovar.openbioinformatics.org/en/latest/
    Forum: https://groups.google.com/forum/#!forum/annovar
    Please cite ANNOVAR paper in your publication:
    Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from
    next-generation sequencing data, Nucleic Acids Research, 38:e164, 2010

    Depends on perl

  17. antiSMASH (antibiotics and Secondary Metabolite Analysis SHell)
  18. module name: antiSMASH
    version 4.0.2

    Genome-wide analysis of gene clusters in bacterial and fungal genomes
    https://bitbucket.org/antismash/antismash/overview
    Web service: http://antismash.secondarymetabolites.org
    Manual: http://docs.antismash.secondarymetabolites.org/

    Includes PFAM and ClusterBlast 20170105_v8_31 databases

  19. Apache Ant
  20. module name: apache-ant
    version 1.9.3
    Other versions: 1.8.4

    Build of Java applications
    http://ant.apache.org/
    Manual: http://ant.apache.org/manual/index.html
    Manual: /group/bioinfo/apps/apps/apache-ant-1.9.3/manual

    Depends on java

  21. ARAGORN
  22. module name: ARAGORN
    version 1.2.38

    tRNA (and tmRNA) detection
    http://mbio-serv2.mbioekol.lu.se/ARAGORN/

    Depends on gcc

  23. ARC (Assembly by Reduced Complexity)
  24. module name: ARC
    version 1.1.3

    Pipeline for iterative, reference guided de novo genome assemblies
    http://ibest.github.io/ARC/
    Forum: https://groups.google.com/forum/#!forum/arc-assembly

    Depends on blat/35-fastq
    Depends on bowtie2
    Depends on spades
    Depends on biopython/2.7.12

  25. Argtable
  26. module name: argtable
    version 2-13

    ANSI C command line parser.
    http://argtable.sourceforge.net/
    man pages available

    Depends on gcc

  27. Artemis
  28. module name: Artemis
    version 15.0.0

    Genome Browser and Annotation Tool
    http://www.sanger.ac.uk/resources/software/artemis/
    Manual: ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf
    Includes act, art and dnaplotter
    Needs X11 support to run GUI

    Depends on java

  29. Aspera Connect Client including ascp
  30. module name: aspera-connect
    version 3.1.1.70545
    Other versions: 3.0.1.64802

    High speed data transfer client for NCBI SRA and other databases
    http://www.ncbi.nlm.nih.gov/books/NBK56561/
    http://www.ncbi.nlm.nih.gov/Traces/sra/
    http://www.ncbi.nlm.nih.gov/books/NBK47527/
    http://wiki.bioinformatics.ucdavis.edu/index.php/Aspera_upload/download_to_NCBI
    http://asperasoft.com/software/transfer-clients/connect-web-browser-plug-in/
    http://downloads.asperasoft.com/download_connect/
    Firefox plug-in in /group/bioinfo/apps/apps/aspera-connect-3.1.1.70545/firefox-plugin
    Copy it to ~/.mozilla/plugins/ to use it
    OpenSSH public key: /group/bioinfo/apps/apps/aspera-connect-3.1.1.70545/etc/asperaweb_id_dsa.openssh

    Depends on gcc

  31. AUGUSTUS
  32. module name: AUGUSTUS
    version 3.2.1
    Other versions: 2.7, 3.0.3, 3.1

    Ab initio gene prediction in eukaryotic genomic sequences
    http://bioinf.uni-greifswald.de/augustus/
    Info: /group/bioinfo/apps/apps/augustus-3.2.1/README.TXT
    Info: /group/bioinfo/apps/apps/augustus-3.2.1/docs
    Web interface: http://bioinf.uni-greifswald.de/augustus/submission

    The program may need to alter its configuration files, so you might
    need put them somewhere else. Follow the procedure below to put the
    config files in your scratch space:

    $ mkdir $RCAC_SCRATCH/augustus
    $ cp -rp $AUGUSTUS_CONFIG_PATH $RCAC_SCRATCH/augustus
    $ export AUGUSTUS_CONFIG_PATH=$RCAC_SCRATCH/augustus/config


    Depends on gcc
    Depends on bamtools/2.4.0

  33. Automatically Tuned Linear Algebra Software (ATLAS)
  34. module name: ATLAS
    version 3.10.1

    http://math-atlas.sourceforge.net/
    compiled with gcc 4.7.2

    Depends on gcc

  35. bambam
  36. module name: bambam
    version 1.4

    Tools for DNA next-gen sequence analysis
    http://udall-lab.byu.edu/Research/Software/BamBam
    Info: /group/bioinfo/apps/apps/bambam-1.4/README


    Depends on gcc
    Depends on perl
    Depends on bamtools/2.4.0
    Depends on htslib/1.3.2
    Depends on zlib/1.2.8

  37. BamM
  38. module name: BamM
    version 1.7.3

    Metagenomics-focused BAM file manipulation
    https://github.com/ecogenomics/BamM
    http://ecogenomics.github.io/BamM/
    Manual: http://ecogenomics.github.io/BamM/manual/BamM_manual.pdf

    Depends on biopython/2.7.12
    Depends on bwa/0.7.12
    Depends on samtools/1.2

  39. BAMStats
  40. module name: BAMStats
    version 1.25

    Interactive desktop GUI tool for summarising Next Generation
    Sequencing alignments
    http://bamstats.sourceforge.net/

    Command line wrapper provided for BAMStats-GUI (e.g. use
    "BAMStats-GUI" to start it with 2 GB of memory)

    Specify the amount of RAM for the programs like this:

    java -Xmx6g -jar /group/bioinfo/apps/apps/BAMStats-1.25/BAMStats-GUI-1.25.jar

    Running the equivalent command line tool:

    java -Xmx4g -jar /group/bioinfo/apps/apps/BAMStats-1.25/BAMStats-1.25.jar -i

    Between 2 and 8 GB of memory, depending on reference size, is
    typically required (specified with the -Xmx flag).


    Depends on java

  41. bamtools
  42. module name: bamtools
    version 2.4.0
    Other versions: 2.1.0-466bc50, 2.2.3, 2.3.0

    Programmer API and an end-user toolkit for handling BAM files
    https://github.com/pezmaster31/bamtools

    Depends on gcc

  43. bamUtil
  44. module name: bamUtil
    version 1.0.10
    Other versions: 1.0.3

    Perform operations on SAM/BAM files
    http://genome.sph.umich.edu/wiki/BamUtil
    Info: http://genome.sph.umich.edu/wiki/BamUtil#Programs


    Depends on gcc

  45. Bandage
  46. module name: Bandage
    version 0.8.1

    Bioinformatics Application for Navigating De novo Assembly Graphs Easily
    https://github.com/rrwick/Bandage
    http://rrwick.github.io/Bandage/
    Documentation: https://github.com/rrwick/Bandage/wiki

    Needs X11 support

  47. Barrnap
  48. module name: barrnap
    version 0.8

    Predicts the location of ribosomal RNA genes in genomes
    http://www.vicbioinformatics.com/software.barrnap.shtml
    https://github.com/tseemann/barrnap/

    Depends on gcc
    Depends on HMMER

  49. BAT (Bisulfite Analyss Toolkit)
  50. module name: BAT
    version 0.1

    Bisulfite sequencing data, differential methylation & downstream analyses
    http://www.bioinf.uni-leipzig.de/Software/BAT/
    https://github.com/helenebioinf/BAT
    Info: http://www.bioinf.uni-leipzig.de/Software/BAT/overview/

    Depends on cutadapt
    Depends on fastqc
    Depends on samtools
    Depends on R-bioconductor/3.4.0
    Depends on perl
    Depends on kentUtils
    Depends on Circos
    Depends on texlive
    Depends on metilene/0.2-4
    Depends on segemehl/0.2.0

  51. Batman
  52. module name: batman
    version alpha-0.2.3
    Other versions: 20090617

    A Bayesian Tool for Methylation Analysis
    http://td-blade.gurdon.cam.ac.uk/software/batman/
    Manual: http://td-blade.gurdon.cam.ac.uk/software/batman/batmanual-alpha-0.2.3.pdf
    You need to be able to write to a MySQL database to use this tool.
    See: http://www.itap.purdue.edu/tlt/careeraccount/mysql.cfm

    Depends on java
    Depends on mysql-connector-java/5.0.5

  53. BayeScan
  54. module name: BayeScan
    version 2.1

    Detecting natural selection from population-based genetic data
    http://cmpg.unibe.ch/software/bayescan/index.html
    Info: http://vcftools.sourceforge.net/docs.html
    Manual: /group/bioinfo/apps/apps/BayeScan-2.1/BayeScan2.1_manual.pdf

    Depends on R-bioconductor

  55. BBMap/BBTools
  56. module name: BBMap
    version 37.38
    Other versions: 31.32, 31.40, 31.56, 32.06, 32.07, 32.14, 32.15, 32.23, 32.27, 32.32, 33.04, 33.08, 33.11, 33.12, 33.13, 33.21, 33.34, 33.40b, 33.41, 33.43, 33.44, 33.46, 33.51, 33.54, 33.57, 33.73b, 34.23, 34.24, 34.25, 34.26, 34.30, 34.33, 34.38, 34.41, 34.46, 34.48, 34.49, 34.56, 34.64, 34.65, 34.72, 34.79, 34.83, 34.86, 34.90, 34.92, 34.94, 34.97, 35.02, 35.07, 35.10, 35.14, 35.24, 35.27, 35.29, 35.32, 35.34, 35.37, 35.38, 35.40, 35.43, 35.49, 35.50, 35.51, 35.59, 35.66, 35.68, 35.69, 35.74, 35.76, 35.80, 35.82, 35.84, 35.85, 35.90, 35.91, 35.92, 36.02, 36.11, 36.14, 36.20, 36.27, 36.28, 36.30, 36.32, 36.38, 36.47, 36.49, 36.59, 36.62, 36.64, 36.66, 36.67, 36.71, 36.73, 36.76, 36.77, 36.81, 36.84, 36.85, 36.86, 36.92, 36.99, 37.02, 37.09, 37.10, 37.17, 37.22, 37.23, 37.24, 37.25, 37.28, 37.31, 37.32, 37.33, 37.34, 37.36

    Short read aligner, and other bioinformatic tools
    http://sourceforge.net/projects/bbmap/
    Info at /group/bioinfo/apps/apps/BBMap-37.38/docs
    Guides at /group/bioinfo/apps/apps/BBMap-37.38/docs/guides
    In particular, see /group/bioinfo/apps/apps/BBMap-37.38/docs/guides/BBMapGuide.txt

    Depends on java
    Depends on samtools

  57. bcftools
  58. module name: bcftools
    version 1.6
    Other versions: 1.3, 1.3.1, 1.4, 1.5

    Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
    http://www.htslib.org/
    Includes support for "bcftools polysomy ..."
    Info: man bcftools

    Depends on gcc
    Depends on gsl/2.3
    Depends on htslib/1.6

  59. bcl2fastq
  60. module name: bcl2fastq
    version 2.20.0.422
    Other versions: 1.8.3, 1.8.4, 2.16.0.10, 2.18.0.12, 2.19.1.403

    illumina BCL2FASTQ Conversion Software
    BCL conversion and demultiplexing of both unzipped and zipped bcl files
    https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
    Manual: /group/bioinfo/apps/apps/bcl2fastq-2.20.0.422/docs/manual.pdf (same as version 2.19)
    Release Notes: /group/bioinfo/apps/apps/bcl2fastq-2.20.0.422/docs/rn.pdf
    License: /group/bioinfo/apps/apps/bcl2fastq-2.20.0.422/docs/EULA.pdf

    Depends on gcc

  61. BEAGLE
  62. module name: beagle
    version 2.1.2
    Other versions: 1260

    General purpose library for evaluating the likelihood of sequence evolution on trees
    https://github.com/beagle-dev/beagle-lib
    http://code.google.com/p/beagle-lib/

    Depends on gcc
    Depends on java

  63. Beagle
  64. module name: Beagle
    version 4.1

    Genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection
    https://faculty.washington.edu/browning/beagle/beagle.html
    Manual: https://faculty.washington.edu/browning/beagle/beagle_4.1_21Jan17.pdf
    Manual: /group/bioinfo/apps/apps/Beagle-4.1/manual.pdf
    Utilities: https://faculty.washington.edu/browning/beagle_utilities/utilities.html

    Start it with: java [options] -jar $BEAGLE_JAR [arguments]

    Also includes bref; use java [options] -jar $BREF_JAR [arguments]

    Depends on java/8

  65. bedops
  66. module name: bedops
    version 2.4.29
    Other versions: 1.2.5, 2.0

    Highly scalable genomic feature operations
    https://github.com/bedops/bedops
    Examples: http://code.google.com/p/bedops/wiki/UsageExamples
    Forum: http://bedops.uwencode.org/forum

    Depends on biopython/2.7.12

  67. BEDTools
  68. module name: BEDTools
    version 2.26.0-35-g6114307
    Other versions: 2.16.2, 2.17.0, 2.20.1, 2.21.0, 2.22.0, 2.25.0

    The swiss army knife for genome arithmetic
    https://github.com/arq5x/bedtools2/
    Manual: http://bedtools.readthedocs.org/en/latest/
    Bugs: https://github.com/arq5x/bedtools2/issues
    Forum at http://groups.google.com/group/bedtools-discuss

    Depends on gcc
    Depends on samtools

  69. Bellman's GAP compiler
  70. module name: gapc
    version 2014.10.07

    GAP-L to C++ translator/compiler
    http://gapc.eu/compiler.html

    Depends on gcc

  71. BESST
  72. module name: BESST
    version 1.3.8
    Other versions: 1.1.2

    Scaffolder for genomic assemblies
    https://github.com/ksahlin/BESST

    Depends on biopython/2.7.8

  73. BFAST
  74. module name: bfast
    version 0.7.0a

    BLAT-like Fast Accurate Search Tool
    http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page
    FAQ: http://sourceforge.net/apps/mediawiki/bfast/index.php?title=FAQ

    Depends on gcc

  75. binutils
  76. module name: binutils
    version 2.30

    Collection of binary tools
    https://www.gnu.org/software/binutils/

    Depends on gcc

  77. bioawk
  78. module name: bioawk
    version 1.0

    BWK awk modified for biological data
    https://github.com/lh3/bioawk

    Depends on gcc

  79. Bioinformatics utilities
  80. module name: ucsc-util
    version Nov-10-2014

    Miscellaneous UCSC Genome Bioinformatics utilities
    http://genome.ucsc.edu/index.html
    http://hgdownload.soe.ucsc.edu/downloads.html
    Manual: /group/bioinfo/apps/apps/ucsc-util-Nov-10-2014/FOOTER
    Manual: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER

    For help on the bigBed and bigWig applications see:
    http://genome.ucsc.edu/goldenPath/help/bigBed.html
    http://genome.ucsc.edu/goldenPath/help/bigWig.html

    Depends on gcc

  81. biom-format
  82. module name: biom-format
    version 1.1.2

    Python module; format for representing counts of observations (e.g.,
    OTUs, KO categories, lipid types) in one or more biological samples
    (e.g., microbiome samples, genomes, metagenomes)
    http://biom-format.org

    Depends on biopython/2.7.3

  83. biotoolbox
  84. module name: biotoolbox
    version 1.19
    Other versions: 1.8.4, 1.8.6

    Tools for querying and analysis of genomic data
    http://code.google.com/p/biotoolbox/
    Wiki: http://code.google.com/p/biotoolbox/w/list

    Depends on perl/5.20.1

  85. Bismark
  86. module name: bismark
    version 0.18.2
    Other versions: 0.10.1, 0.14.2, 0.14.5, 0.17.0

    Map bisulfite converted sequence reads and determine cytosine methylation states
    http://www.bioinformatics.babraham.ac.uk/projects/bismark/
    https://github.com/FelixKrueger/Bismark
    Manual: /group/bioinfo/apps/apps/Bismark-0.18.2/Docs/README.md
    Manual: https://github.com/FelixKrueger/Bismark/tree/master/Docs

    Depends on perl
    Depends on bowtie
    Depends on bowtie2
    Depends on samtools

  87. BLASR
  88. module name: blasr
    version 1.3.1

    https://github.com/PacificBiosciences/blasr
    The PacBio long read aligner

    Depends on HDF5/1.8.14

  89. blast2html
  90. module name: blast2html
    version 82b8c9722996

    Blast XML to HTML conversion tool
    https://toolshed.g2.bx.psu.edu/repository/view_repository?changeset_revision=82b8c9722996&id=f32220daa6f46e04
    Info: /group/bioinfo/apps/apps/blast2html-82b8c9722996/README.rst

    Depends on biopython/2.7.8

  91. BLAT
  92. module name: blat
    version 35
    Other versions: 34, 35-fastq

    Alignment tool like BLAST
    http://genome.ucsc.edu/FAQ/FAQblat.html
    Manual: http://genome.ucsc.edu/goldenPath/help/blatSpec.html

    Depends on gcc

  93. BLESS
  94. module name: BLESS
    version 0.15

    Bloom-filter-based Error Correction Tool for NGS reads
    http://sourceforge.net/projects/bless-ec/
    Info: /group/bioinfo/apps/apps/BLESS-0.15/README

    Depends on gcc

  95. boost
  96. module name: Boost
    version 1_54_0
    Other versions: 1.50.0, 1.54.0, 1.63.0, 1.65.1

    Portable C++ source libraries
    http://www.boost.org/

    Depends on gcc

  97. Bowtie
  98. module name: bowtie
    version 1.2.0
    Other versions: 0.11.3, 0.12.7, 0.12.8, 0.12.9, 1.0.0, 1.0.1, 1.1.0, 1.1.1, 1.1.2

    An ultrafast memory-efficient short read aligner
    http://bowtie-bio.sourceforge.net/index.shtml
    Manual: http://bowtie-bio.sourceforge.net/manual.shtml
    Manual: /group/bioinfo/apps/apps/bowtie-1.2-try2/MANUAL
    Tutorial: http://bowtie-bio.sourceforge.net/tutorial.shtml
    Tutorial: /group/bioinfo/apps/apps/bowtie-1.2-try2/TUTORIAL

    Depends on tbb

  99. Bowtie2
  100. module name: bowtie2
    version 2.3.3.1
    Other versions: 2.0.0-beta5, 2.0.0-beta6, 2.0.0-beta7, 2.0.1, 2.0.2, 2.0.3, 2.0.4, 2.0.5, 2.0.6, 2.1.0, 2.2.0, 2.2.1, 2.2.2, 2.2.3, 2.2.4, 2.2.5, 2.2.6, 2.2.7, 2.2.8, 2.2.9, 2.3.0, 2.3.1, 2.3.2

    Fast and sensitive read alignment
    http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
    Manual: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
    Manual: /group/bioinfo/apps/apps/bowtie2-2.3.3.1/MANUAL
    FAQ: http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml

    Depends on gcc
    Depends on tbb
    Depends on zlib
    Depends on perl

  101. BppSuite & Bio++ libraries
  102. module name: BppSuite
    version 2.2.0

    Bioinformatics libraries & programs (sequence analysis, phylogenetics, molecular evolution and population genetics)
    http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
    https://github.com/BioPP

    Depends on gcc
    Depends on texinfo

  103. BRAKER1
  104. module name: BRAKER
    version 1.9
    Other versions: 1.8

    Pipeline for unsupervised RNA-Seq-based genome annotation
    http://bioinf.uni-greifswald.de/augustus/downloads/
    Info: /group/bioinfo/apps/apps/BRAKER-1.9/README.braker
    Example data: $BRAKER_PATH/example

    Run the "init_augustus" script from AUGUSTUS/3.1 before using BRAKER
    That will set $AUGUSTUS_CONFIG_PATH to point to directory where
    program can write files.


    Depends on AUGUSTUS/3.1
    Depends on GeneMark/4.32
    Depends on samtools/1.2
    Depends on perl

  105. BreakDancer
  106. module name: BreakDancer
    version 1.1.2

    Genome-wide detection of structural variants from next generation paired-end sequencing reads
    http://breakdancer.sourceforge.net/index.html

    Depends on perl

  107. Bridger
  108. module name: Bridger
    version 2014-12-01

    Framework for de novo transcriptome assembly using RNA-seq data
    https://github.com/fmaguire/Bridger_Assembler
    https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0596-2

    Depends on Boost

  109. Brownie
  110. module name: brownie
    version 2017-09-07

    Corrects sequence reads
    https://github.com/biointec/brownie
    Manual: https://github.com/biointec/brownie/wiki

    Depends on gcc

  111. BUSCO (Benchmarking Universal Single-Copy Orthologs)
  112. module name: BUSCO
    version 2.0-2017-02-15
    Other versions: 1.1b1

    Assess genome assembly and annotation completeness
    http://busco.ezlab.org/
    User Guide: http://gitlab.com/ezlab/busco/raw/master/BUSCO_v2.0_userguide.pdf
    User Guide: /group/bioinfo/apps/apps/BUSCO_2.0-2017-02-15/BUSCO_v2.0_userguide.pdf

    Invoke script with "BUSCO"

    Depends on biopython/2.7.12
    Depends on AUGUSTUS/3.2.1
    Depends on blast
    Depends on HMMER/3.1b2
    Depends on EMBOSS

  113. bwa
  114. module name: bwa
    version 0.7.15
    Other versions: 0.5.9, 0.6.1, 0.6.2, 0.7.10, 0.7.12, 0.7.5a

    Burrows-Wheeler Aligner (BWA)
    http://sourceforge.net/projects/bio-bwa/
    http://bio-bwa.sourceforge.net/
    Manual: http://bio-bwa.sourceforge.net/bwa.shtml
    or using "man bwa"
    Info: /group/bioinfo/apps/apps/bwa-0.7.15/README.md
    Info: /group/bioinfo/apps/apps/bwa-0.7.15/doc/README.md
    Info: /group/bioinfo/apps/apps/bwa-0.7.15/doc/NEWS.md

    Depends on gcc
    Depends on perl
    Depends on zlib

  115. bzip2
  116. module name: bzip2
    version 1.0.6

    bzip2 is a freely available, patent free, high-quality data compressor
    Includes shared library
    http://www.bzip.org/
    man pages available


    Depends on gcc

  117. CAMSA
  118. module name: CAMSA
    version 1.0.0
    Other versions: 1.1.0b14

    Comparative Analysis and Merging of Scaffold Assemblies
    https://github.com/compbiol/CAMSA

    Depends on biopython/2.7.12

  119. Canu
  120. module name: canu
    version 1.6
    Other versions: 1.4

    Fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION)
    https://github.com/marbl/canu
    Manual: http://canu.readthedocs.io/en/latest/index.html
    Info: http://biorxiv.org/content/early/2016/08/24/071282
    Info: https://www.youtube.com/watch?v=iiLj1vpuCRA

    Depends on perl
    Depends on java/8

  121. CAP3
  122. module name: CAP3
    version 12.21.07

    Genome assembly
    http://seq.cs.iastate.edu/
    Manual: /group/bioinfo/apps/apps/CAP3-12.21.07/doc

    Depends on gcc

  123. CASAVA
  124. module name: CASAVA
    version 1.8.2
    Other versions: 1.8.0

    Consensus Assessment of Sequence And VAriation
    Processes sequencing reads provided by RTA or OLB
    http://www.illumina.com/support/sequencing/sequencing_software/casava.ilmn
    Info at /group/bioinfo/apps/apps/CASAVA-1.8.2/share/CASAVA-1.8.2/docs/casava

    Depends on gcc

  125. CASPER (Context-Aware Scheme for Paired-End Read)
  126. module name: CASPER
    version 0.8.2

    Pair-end read merger
    http://best.snu.ac.kr/casper/

    Depends on gcc
    Depends on jellyfish

  127. CD-HIT
  128. module name: cd-hit
    version 4.6.5-2016-0304
    Other versions: 3.1.1, 4.6.1-2012-08-27, 4.6.1-2012-08-27-openmp, 4.6-2012-04-25

    Clustering and comparing protein or nucleotide sequences
    Includes "AuxTools"
    http://weizhong-lab.ucsd.edu/cd-hit/
    https://github.com/weizhongli/cdhit
    Docs: http://weizhong-lab.ucsd.edu/cd-hit/doc.php
    Info: /group/bioinfo/apps/apps/cd-hit-v4.6.5-2016-0304/doc
    User Guide: /group/bioinfo/apps/apps/cd-hit-v4.6.5-2016-0304/cd-hit-user-guide.pdf

    Depends on gcc

  129. cdbtools
  130. module name: cdbtools
    version 0.99

    FASTA file indexing and entry retrieval
    cdbfasta and cdbyank programs
    Info: /group/bioinfo/apps/apps/cdbtools-0.99/README

  131. CEAS
  132. module name: CEAS
    version 1.0.2
    Other versions: 1.0.2a, 1.0.2b

    Cis-regulatory Element Annotation System
    http://liulab.dfci.harvard.edu/CEAS/

    Depends on biopython/2.7.3

  133. CEGMA (Core Eukaryotic Genes Mapping Approach)
  134. module name: cegma
    version 2.5
    Other versions: 2.4.010312

    Pipeline for building a set of gene annotations in virtually any eukaryotic genome
    http://korflab.ucdavis.edu/Datasets/cegma/
    Info: /group/bioinfo/apps/apps/cegma-2.5/README.md
    Info: /group/bioinfo/apps/apps/cegma-2.5/release_notes.md


    Depends on gcc
    Depends on blast/2.2.29+
    Depends on HMMER
    Depends on genewise
    Depends on geneid

  135. Celera Assembler
  136. module name: wgs-assembler
    version 8.3rc1

    de novo whole-genome shotgun (WGS) DNA sequence assembler
    http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page
    Info: http://wgs-assembler.sourceforge.net/wiki/index.php/Help
    License: /group/bioinfo/apps/apps/wgs-8.3rc1/LICENSE.txt

    Depends on gcc

  137. Cell Ranger: Pipelines
  138. module name: cellranger
    version 2.1.0
    Other versions: 2.0.2

    Analysis pipelines for sample demultiplexing, barcode processing, and single cell 3’ gene counting
    https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
    Release notes: https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/2-1

    Using this software means you agree to the license at:
    https://support.10xgenomics.com/docs/license

    Reference data in /group/bioinfo/apps/apps/cellranger-2.1.0/references

    Send questions about the software to support@10xgenomics.com


    Depends on bcl2fastq
    Depends on java

  139. CellProfiler
  140. module name: CellProfiler
    version 2.2.0

    http://cellprofiler.org/
    Quantitatively measure phenotypes from images automatically

    Depends on gcc
    Depends on tcl
    Depends on igraph
    Depends on HDF5/1.8.14
    Depends on java
    Depends on R-bioconductor/3.1.0

  141. Censor
  142. module name: censor
    version 4.2.29

    Compares and masks protein or nucleotide sequences
    http://www.girinst.org/downloads/software/censor/

    Includes copy of Repbase
    No support for WU-BLAST; only censor.ncbi available

    Depends on perl
    Depends on blast/2.2.28+

  143. CentroidFold
  144. module name: centroid_fold
    version 0.0.9

    Predict RNA secondary structures based on a generalized centroid estimator
    MCL algorithm finds cluster structure in graphs
    http://www.ncrna.org/software/centroidfold
    http://www.ncrna.org/software/centroidfold/download/
    Info: /group/bioinfo/apps/apps/centroid_fold-0.0.9/README.html

  145. CFITSIO
  146. module name: CFITSIO
    version 3.370

    FITS File Subroutine Library
    http://heasarc.gsfc.nasa.gov/fitsio/
    man pages available

    Depends on gcc

  147. CIRCexplorer
  148. module name: CIRCexplorer
    version 1.1.10
    Other versions: 1.1.3, 2.2.6

    Circular RNA analysis toolkits
    http://yanglab.github.io/CIRCexplorer/
    FAQ: https://github.com/YangLab/CIRCexplorer/wiki/FAQ

    Depends on biopython/2.7.12
    Depends on tophat
    Depends on STAR
    Depends on BEDTools
    Depends on samtools

  149. Circos
  150. module name: Circos
    version 0.69-2
    Other versions: 0.67-1

    Visualize data in a circular layout
    http://www.circos.ca/
    Manual: http://www.circos.ca/documentation/

    Depends on perl/5.20.1

  151. clearcut
  152. module name: clearcut
    version 1.0.9

    Reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm
    http://www.mothur.org/wiki/Clearcut
    Info: /group/bioinfo/apps/apps/clearcut-1.0.9/README
    Info: /group/bioinfo/apps/apps/clearcut-1.0.9/examples

  153. CleaveLand
  154. module name: CleaveLand
    version 4.3
    Other versions: 3.0.1

    Pipeline for finding cleaved small RNA targets using degradome data
    a.k.a PARE (Parallel Analysis of RNA Ends) and GMUCT (Genome-wide Mapping of
    Uncapped Transcripts).
    http://axtell-lab-psu.weebly.com/cleaveland.html
    Info: /group/bioinfo/apps/apps/CleaveLand-4.3/CleaveLand4_TUTORIAL.pdf
    Tutorial: http://axtelldata.bio.psu.edu/data/CleaveLand4_Tutorial/

    Depends on perl
    Depends on bowtie
    Depends on ViennaRNA
    Depends on samtools/1.2
    Depends on R-bioconductor/3.1.2

  155. CLIPper
  156. module name: CLIPper
    version 0.2.0

    A tool to identify CLIP-seq peaks?
    https://github.com/YeoLab/clipper
    https://github.com/YeoLab/clipper/wiki/CLIPper-Home
    Forum: https://groups.google.com/forum/?fromgroups#!forum/clipper-discuss

    Depends on biopython/2.7.11

  157. CLUMPP
  158. module name: CLUMPP
    version 1.1.2

    Deals with label switching and multimodality problems in
    population-genetic cluster analyses
    http://www.stanford.edu/group/rosenberglab/clumpp.html
    Manual: /group/bioinfo/apps/apps/CLUMPP-1.1.2/CLUMPP_Manual.pdf

    Depends on gcc

  159. Clustal Omega
  160. module name: clustalo
    version 1.2.1
    Other versions: 1.1.0

    Multiple sequence alignment
    http://www.clustal.org/omega/

    Depends on argtable

  161. ClustalW2
  162. module name: clustalw
    version 2.1

    Multiple sequence alignment
    http://www.ebi.ac.uk/Tools/msa/clustalw2/

    Depends on gcc

  163. CMake
  164. module name: cmake
    version 3.9.4

    Build, test and package software
    https://cmake.org/

    Depends on gcc

  165. CNVer
  166. module name: CNVer
    version 0.8.1

    Method for Detecting Copy Number Variation
    http://compbio.cs.toronto.edu/CNVer/
    Forum: http://groups.google.com/group/cnver-users
    Manual: /group/bioinfo/apps/apps/cnver-0.8.1/README-0.8.1.txt
    Manual: http://compbio.cs.toronto.edu/cnver/README-0.8.1.txt
    hg18 data: /group/bioinfo/apps/apps/cnver-0.8.1/hg18comp.tar.gz
    hg19 data: /group/bioinfo/apps/apps/cnver-0.8.1/hg19comp.tar.gz

    Depends on gcc

  167. CNVnator
  168. module name: CNVnator
    version 0.3

    http://avrilomics.blogspot.com/2013/01/using-cnvnator-to-find-copy-number.html
    Identify copy number variations (CNVs) in a genome
    Citation: http://www.ncbi.nlm.nih.gov/pubmed/21324876

    Depends on ROOT

  169. consed
  170. module name: consed
    version 29.0
    Other versions: 23.0, 24.0, 25.0, 26.0, 27.0, 28.0

    A sequence finishing package
    http://bozeman.mbt.washington.edu/consed/consed.html
    Manual: http://bozeman.mbt.washington.edu/consed/distributions/README.28.0.txt
    Info in /group/bioinfo/apps/apps/consed-29.0/README.txt
    Needs X11 support for GUI

    Depends on cross_match/1.090518
    Depends on phred

  171. CONTIGuator
  172. module name: CONTIGuator
    version 2.7.5

    https://github.com/combogenomics/CONTIGuator
    Bacterial genomes finishing tool for structural insights on draft genomes


    Depends on biopython/2.7.12
    Depends on blast
    Depends on perl
    Depends on MUMmer
    Depends on primer3

  173. Control-FREEC
  174. module name: freec
    version 7.0
    Other versions: 5.5, 5.9

    A tool for detection of copy-number changes and
    allelic imbalances (including LOH) using deep-sequencing data
    http://bioinfo-out.curie.fr/projects/freec
    Tutorial at http://bioinfo-out.curie.fr/projects/freec/tutorial.html


    Depends on gcc

  175. corset
  176. module name: corset
    version 1.03

    Clustering de novo assembled transcripts and counting overlapping reads
    https://code.google.com/p/corset-project/
    Example: https://code.google.com/p/corset-project/wiki/Example
    Forum: https://groups.google.com/forum/#!forum/corset-project

    Depends on gcc

  177. cortex_var
  178. module name: cortex_var
    version 1.0.5.21
    Other versions: 1.0.5.20

    Tool for genome assembly and variation analysis
    http://cortexassembler.sourceforge.net/index_cortex_var.html
    Manual: http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf

    Depends on gsl/1.15
    Depends on stampy/1.0.26
    Depends on vcftools/0.1.12b

  179. cppunit
  180. module name: cppunit
    version 1.13.2
    Other versions: 1.12.0, 1.12.1

    C++ port of the JUnit framework for unit testing
    https://www.freedesktop.org/wiki/Software/cppunit/

    Depends on gcc

  181. CRI-MAP Improved
  182. module name: crimap
    version 2.507
    Other versions: 2.4, 2.504a

    Genetic linkage analysis of diploid species
    http://www.animalgenome.org/tools/share/crimap/
    Forum: http://www.animalgenome.org/community/crimap-users
    Info in /group/bioinfo/apps/apps/crimap-2.507/doc directory

    Depends on gcc

  183. CRISP
  184. module name: CRISP
    version 122713

    Multi-sample variant caller for high-throughput pooled sequence data
    https://sites.google.com/site/vibansal/software/crisp
    Info: /group/bioinfo/apps/apps/CRISP-122713/README

  185. cross_match
  186. module name: cross_match
    version 1.080812
    Other versions: 1.090518

    Compare DNA sequences
    http://www.phrap.org/phredphrapconsed.html
    Manual: http://www.phrap.org/phredphrap/general.html
    Info in /group/bioinfo/apps/apps/genome/doc
    Also includes phred (v0.020425.c), phrap (v1.080812), consed (v19.0)

  187. CrossMap
  188. module name: CrossMap
    version 0.2.4

    Conversion of genome coordinates (or annotation files) between different assemblies
    http://crossmap.sourceforge.net

    Depends on biopython/2.7.11

  189. Cufflinks
  190. module name: cufflinks
    version 2.2.1
    Other versions: 0.7.0, 1.0.3, 1.1.0, 1.2.0, 1.2.1, 1.3.0, 2.0.0, 2.0.2, 2.1.0, 2.1.1, 2.2.0, 2.2.1-t1

    Transcript assembly, differential expression, and differential regulation for RNA-Seq
    http://cufflinks.cbcb.umd.edu/
    Manual: http://cufflinks.cbcb.umd.edu/manual.html
    FAQ: http://cufflinks.cbcb.umd.edu/faq.html

    Depends on zlib

  191. cURL and libcurl
  192. module name: curl
    version 7.46.0

    Command line tool and library for transferring data with URL syntax
    http://curl.haxx.se/
    man curl

    Depends on gcc

  193. cutadapt
  194. module name: cutadapt
    version 1.9.1
    Other versions: 1.12, 1.13, 1.1a, 1.1b, 1.2.1

    Removes adapter sequences from DNA sequencing reads
    https://cutadapt.readthedocs.org/en/stable/

    Depends on biopython/2.7.8

  195. Cytoscape
  196. module name: Cytoscape
    version 2.8.3

    Network Data Integration, Analysis, and Visualization in a Box
    http://www.cytoscape.org/
    http://www.cytoscape.org/what_is_cytoscape.html
    Wiki: http://wiki.cytoscape.org/
    Manual: /group/bioinfo/apps/apps/Cytoscape-2.8.3/docs/manual.pdf


    Depends on java

  197. DANPOS
  198. module name: DANPOS
    version 2.2.2

    A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing
    https://sites.google.com/site/danposdoc/
    Manual: https://sites.google.com/site/danposdoc/home

    Depends on biopython/2.7.8

  199. DBG2OLC
  200. module name: DBG2OLC
    version 12-08-2015
    Other versions: 12-08-2105

    Assembly of Large Genomes Using the Compressed Overlap Graph
    https://sourceforge.net/projects/dbg2olc/
    Manual: /group/bioinfo/apps/apps/DBG2OLC-12-08-2015/DBG2OLC_Manual.docx

  201. dbHT-Trans
  202. module name: dbHT-Trans
    version 14-Jul-2016

    Filtering the Protein-Encoding Transcripts
    http://www.ncbi.nlm.nih.gov/pubmed/26484655
    https://github.com/chengroup/dbHT-Trans
    Manual: /group/bioinfo/apps/apps/dbHT-Trans-14-Jul-2016/manual.pdf

    This software doesn't seem to work

    Need to configure MySQL database prior to using this software
    Need to copy script into your home directory and run from there:

    $ cp -rp $dThome ~/.
    $ cd ~/dbHT-Trans-14-Jul-2016
    $ # edit config.txt with MySQL server info
    $ python config.py
    $ ./dbHT-Trans-Operator ...


    Depends on biopython/2.7.11

  203. DeconSeq
  204. module name: deconseq
    version 0.4.3
    Other versions: 0.4.1, 0.4.2

    DECONtamination of SEQuence data using a modified version of BWA
    http://deconseq.sourceforge.net
    Info at /group/bioinfo/apps/apps/deconseq-standalone-0.4.3/README
    FAQ: http://deconseq.sourceforge.net/faq.html
    Manual; http://deconseq.sourceforge.net/manual.html

    Based on BWA (Burrows-Wheeler Aligner) Version: 0.5.9-r16
    Probably need to make copy of deconseq.pl and DeconSeqConfig.pm files
    from /group/bioinfo/apps/apps/deconseq-standalone-0.4.3
    Modify the DeconSeqConfig.pm file as necessary.

    Depends on perl

  205. deepTools
  206. module name: deeptools
    version 2.2.4
    Other versions: 1.5.12

    Tools to process and analyze deep sequencing data.
    https://github.com/fidelram/deepTools
    Wiki: https://github.com/fidelram/deepTools/wiki

    Depends on biopython/2.7.8
    Depends on samtools

  207. DejaGnu
  208. module name: dejagnu
    version 1.6

    Framework for testing other programs
    https://www.gnu.org/software/dejagnu/

  209. DELLY
  210. module name: DELLY
    version 0.7.2
    Other versions: 0.6.1

    https://github.com/tobiasrausch/delly
    Structural variant discovery by integrated paired-end and split-read analysis
    Forum: http://groups.google.com/d/forum/delly-users

    Use "delly" to run the program.

    To use multithreaded, OpenMP version, use "delly-parallel"
    Set the environment variable OMP_NUM_THREADS to the number of threads you want
    to use before running.

    Depends on PyVCF

  211. DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation)
  212. module name: detonate
    version 1.10
    Other versions: 1.8.1

    Evaluate de novo transcriptome assemblies
    http://deweylab.biostat.wisc.edu/detonate/
    Tutorial: /group/bioinfo/apps/apps/detonate-1.10/VIGNETTE
    Tutorial example data at /group/bioinfo/apps/apps/detonate-1.10/rsem-eval/true_transcript_length_distribution

    Depends on gcc
    Depends on bowtie
    Depends on blat
    Depends on rsem

  213. DIALIGN-TX
  214. module name: DIALIGN-TX
    version 1.0.2

    Segment-based multiple sequence alignment
    http://dialign-tx.gobics.de/

    Depends on perl
    Depends on gcc

  215. DIAMOND
  216. module name: diamond
    version 0.8.36
    Other versions: 0.6.12, 0.7.1, 0.7.8, 0.7.9, 0.9.6

    Align short DNA sequencing reads to a protein reference database such as NCBI-NR
    http://ab.inf.uni-tuebingen.de/software/diamond/
    Manual: https://github.com/bbuchfink/diamond/blob/master/README.rst
    Manual: /group/bioinfo/apps/apps/diamond-0.8.36/diamond_manual.pdf

    Includes Mar 3 2017 NCBI nr database data at $DIAMONDDB/nr.dmnd
    Includes Feb 23 2017 NCBI refseq_protein data at $DIAMONDDB/refseq_protein.dmnd

  217. diffReps
  218. module name: diffReps
    version 1.55.6
    Other versions: 1.55.4

    Differential analysis for ChIP-seq with biological replicates
    https://github.com/shenlab-sinai/diffreps
    Forum: https://groups.google.com/forum/?fromgroups%5C#!forum/diffreps-discuss

    Depends on perl/5.20.1

  219. DiNuP
  220. module name: DiNuP
    version 1.3

    A Systematic Approach to Identify Regions of Differential Nucleosome Positioning
    http://www.tongji.edu.cn/~zhanglab/DiNuP/index.html

    Depends on biopython/2.7.8

  221. DISCOVAR
  222. module name: discovar
    version 52488
    Other versions: 48686, 52415

    Genome assembler and variant caller
    http://www.broadinstitute.org/software/discovar/blog/
    FAQ: http://www.broadinstitute.org/software/discovar/blog/?page_id=23
    License: /group/bioinfo/apps/apps/discovar-52488/share/doc/discovar/LICENSE
    Forum: https://groups.google.com/a/broadinstitute.org/forum/?hl=en&fromgroups#!forum/discovar-user-forum
    Manual: https://docs.google.com/document/d/1U_o-Z0dJ0QKiJn86AV2o_YHiFzUtW9c57eh3tYjkINc/edit?usp=sharing
    Example data in /group/bioinfo/apps/apps/discovar-52488/examples

    Depends on gcc
    Depends on picard-tools
    Depends on samtools
    Depends on biopython/2.7.3

  223. DISCOVAR de novo
  224. module name: discovardenovo
    version 52488
    Other versions: 52415

    Large genome assembler
    http://www.broadinstitute.org/software/discovar/blog/
    FAQ: http://www.broadinstitute.org/software/discovar/blog/?page_id=23
    Forum: https://groups.google.com/a/broadinstitute.org/forum/?hl=en&fromgroups#!forum/discovar-user-forum
    Manual: https://docs.google.com/document/d/1U_o-Z0dJ0QKiJn86AV2o_YHiFzUtW9c57eh3tYjkINc/edit?usp=sharing
    Manual: /group/bioinfo/apps/apps/discovardenovo-52488/share/doc/discovardenovo
    Example data in /group/bioinfo/apps/apps/discovardenovo-52488/examples

    Depends on gcc
    Depends on samtools
    Depends on jemalloc

  225. DISLIN
  226. module name: DISLIN
    version 11.0
    Other versions: 10.5

    Plotting library for displaying data
    http://www.mps.mpg.de/dislin/

    Probably need X11 support

    Depends on gcc

  227. distruct
  228. module name: distruct
    version 1.1

    Graphically display results produced by the genetic
    clustering program "Structure"
    http://www.stanford.edu/group/rosenberglab/distruct.html
    Manual: /group/bioinfo/apps/apps/distruct-1.1/distructManual.pdf

    Depends on gcc

  229. DLCpar
  230. module name: DLCpar
    version 1.0

    Reconciliation method for inferring gene duplications, losses, and coalescence
    Python module
    https://www.cs.hmc.edu/~yjw/software/dlcpar/

    Depends on biopython/2.7.12

  231. dna-bison
  232. module name: dna-bison
    version 0.3.3b
    Other versions: 0.2, 0.2.4, 0.3.0, 0.3.1, 0.3.2, 0.3.2b, 0.3.3

    Bisulfite alignment On Nodes of a cluster
    http://sourceforge.net/projects/dna-bison/
    wiki: http://sourceforge.net/p/dna-bison/wiki/Home/
    Tutorial: /group/bioinfo/apps/apps/dna-bison-0.3.3b/bison_tutorial

    Depends on gcc
    Depends on openmpi
    Depends on biopython/2.7.8
    Depends on bowtie2
    Depends on R-bioconductor/3.1.0

  233. DOTS-Finder
  234. module name: DOTS-Finder
    version 1.0

    Driver Oncogenes and Tumor Suppressors Finder
    http://cgsb.genomics.iit.it/wiki/projects/DOTS-Finder
    http://sourceforge.net/projects/dotsfinder/
    Manual: http://cgsb.genomics.iit.it/wiki/projects/DOTS-Finder/Documentation
    Sample files; /group/bioinfo/apps/apps/DOTS-Finder-1.0/sample-files

    Depends on biopython/2.7.8

  235. ea-utils
  236. module name: ea-utils
    version 1.1.2-537
    Other versions: 1.1.2-408

    FASTQ processing utilities
    http://code.google.com/p/ea-utils/
    wiki: http://code.google.com/p/ea-utils/w/list

    Depends on gcc
    Depends on bamtools
    Depends on gsl

  237. EDGE-pro
  238. module name: EDGE-pro
    version 1.3.1

    Prokaryotic transcriptome analysis system
    http://www.ccb.jhu.edu/software/EDGE-pro/index.shtml
    Manual: http://www.ccb.jhu.edu/software/EDGE-pro/MANUAL
    Manual: /group/bioinfo/apps/apps/EDGE_pro_v1.3.1/MANUAL
    Example data: /group/bioinfo/apps/apps/EDGE_pro_v1.3.1/example

    Modified edge.pl to remove -s switch

    The edge.pl script does not need to be in working directory nor should
    you invoke it as PATH/edge.pl as described in manual.


    Depends on gcc
    Depends on bowtie2

  239. edittag
  240. module name: edittag
    version 1.1

    Edit distance sequence tags and helpers
    https://github.com/faircloth-lab/edittag/
    http://faircloth-lab.github.io/edittag/

    Depends on biopython/2.7.12
    Depends on mod-primer3

  241. elinks
  242. module name: elinks
    version 0.12pre5

    text mode web browser
    http://elinks.or.cz/
    man: elinks, elinkskeys, elinks.conf
    copied from elinks-0.12-0.21.pre5.el6_3.x86_64

    Depends on gcc

  243. EMBOSS
  244. module name: EMBOSS
    version 6.6.0-t2
    Other versions: 6.4.0, 6.5.7, 6.6.0

    The European Molecular Biology Open Software Suite
    http://emboss.sourceforge.net/
    Info: http://emboss.sourceforge.net/docs/
    Info: http://emboss.sourceforge.net/news/
    Info: /group/bioinfo/apps/apps/EMBOSS-6.6.0-t2/share/EMBOSS/doc/

    Includes REBASE 702 data

    Get Jemboss GUI with "runJemboss.sh"; need X11 support

    Depends on gcc
    Depends on java

  245. EMIRGE (Expectation-Maximization Iterative Reconstruction of Genes from the Environment)
  246. module name: EMIRGE
    version 0.61.0

    Reconstructs full length ribosomal genes from short read sequencing data.
    https://github.com/csmiller/EMIRGE
    Issues: https://github.com/csmiller/EMIRGE/issues
    Forum: https://groups.google.com/forum/#!forum/emirge-users

    Depends on biopython/2.7.12
    Depends on bowtie/1.1.2
    Depends on vsearch
    Depends on usearch/8

  247. EMMAX
  248. module name: EMMAX
    version 20120210

    Statistical test for large scale human or model organism association
    mapping accounting for the sample structure.
    http://genome.sph.umich.edu/wiki/EMMAX

    Depends on gcc
    Depends on ATLAS

  249. epic
  250. module name: bioepic
    version 0.1.25

    Diffuse domain ChIP-Seq caller based on SICER
    https://github.com/biocore-ntnu/epic
    Forum: https://groups.google.com/forum/#!forum/epic-chip-seq

    Depends on biopython/2.7.12
    Depends on jellyfish

  251. EvidentialGene (tr2aacds.pl)
  252. module name: EvidentialGene
    version 2017-02-13

    mRNA Transcript Assembly
    http://arthropods.eugenes.org/EvidentialGene/
    http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly

    Just set up for tr2aacds.pl script
    Probably doesn't work

    Depends on perl
    Depends on exonerate
    Depends on cd-hit
    Depends on blast

  253. Exonerate
  254. module name: exonerate
    version 2.2.0

    Generic tool for sequence alignment
    http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
    Use "man exonerate" for more info
    Users guide: http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-user-guide
    Manual: http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-manual


    Depends on gcc

  255. expat
  256. module name: expat
    version 2.1.0

    XML Parser
    http://sourceforge.net/projects/expat/
    man pages available

    Depends on gcc

  257. eXpress
  258. module name: express
    version 1.5.1

    Streaming quantification for high-throughput sequencing
    http://bio.math.berkeley.edu/eXpress/
    Info: /group/bioinfo/apps/apps/express-1.5.1/README

    Depends on gcc

  259. FALCON
  260. module name: FALCON
    version 2017-06-28

    Experimental PacBio diploid assembler
    https://github.com/PacificBiosciences/FALCON
    Info: https://github.com/PacificBiosciences/FALCON/wiki
    Manual: https://github.com/PacificBiosciences/FALCON/wiki/Manual

    This probably does not work

    Depends on biopython/2.7.12

  261. FASconCAT
  262. module name: FASconCAT
    version 1.0

    Concatenate sequence fragments into a supermatrix file for phylogenetic purposes
    http://zfmk.de/web/Forschung/Abteilungen/AG_Wgele/Software/FASconCAT/index.en.html
    Manual: /group/bioinfo/apps/apps/FASconCAT-1.0/FASconCAT_Manual.pdf
    Manual: http://www.zfmk.de/bioinformatics/FASconCAT_Manual.pdf

    Depends on perl

  263. FAST-iCLIP
  264. module name: FAST-iCLIP
    version 0.9.1
    Other versions: 0.9.3, 2017-11-29

    Fully Automated and Standardized (FAST) iCLIP analysis pipeline.
    https://github.com/ChangLab/FAST-iCLIP
    Probably doesn't work

    Depends on biopython/2.7.11
    Depends on bowtie2
    Depends on STAR
    Depends on BEDTools
    Depends on fastx

  265. FASTA
  266. module name: fasta
    version 36.3.5e
    Other versions: 35, 35.4.12

    Identify statistically significant sequence similarity that can be used to infer homology
    Similar to NCBI BLAST
    http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml
    Manual: http://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf
    Manual: man fasta36

    Depends on gcc

  267. Fasta Utilities
  268. module name: fasta_utilities
    version 30-Nov-2015
    Other versions: 9-May-2014

    A collection of scripts developed to interact with fasta, fastq and sam/bam files.
    https://github.com/jimhester/fasta_utilities
    Use man command to read provided man pages


    Depends on perl
    Depends on samtools

  269. FastaGrep
  270. module name: fastagrep
    version 2.0

    Search oligonucleotide binding sites from genomic sequences
    http://bioinfo.ut.ee/?page_id=167
    Manual at /group/bioinfo/apps/apps/fastagrep-2.0/README_fg.txt

    Depends on gcc

  271. fastq-pair
  272. module name: fastq-pair
    version 0.1

    Rewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons
    https://github.com/linsalrob/fastq-pair
    https://edwards.sdsu.edu/research/sorting-and-paring-fastq-files/


    Depends on gcc

  273. fastq_screen
  274. module name: fastq_screen
    version 0.5.2
    Other versions: 0.4.2

    Contamination Screening for large data sets
    http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
    Info: /group/bioinfo/apps/apps/fastq_screen_v0.5.2/README.txt
    Info: /group/bioinfo/apps/apps/fastq_screen_v0.5.2/RELEASE_NOTES.txt

    Need to create configuration file and add databases:
    - cp /group/bioinfo/apps/apps/fastq_screen_v0.5.2/fastq_screen.conf.example ~/fastq_screen.conf
    - edit fastq_screen.conf in your home directory
    - fastq_screen --conf ~/fastq_screen.conf

    Depends on perl
    Depends on bowtie
    Depends on bowtie2

  275. FastQC
  276. module name: fastqc
    version 0.11.5
    Other versions: 0.10.0, 0.10.1, 0.11.2

    Quality control application for high throughput sequence data
    http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    Manual: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/

    Depends on java

  277. fastStructure
  278. module name: fastStructure
    version 1.0.x

    Framework for inferring population structure from SNP genotype data.
    http://rajanil.github.io/fastStructure/
    Use "structure.py" to start program

    Depends on biopython/2.7.11
    Depends on gsl

  279. FastTree
  280. module name: FastTree
    version 2.1.7
    Other versions: 2.1.3, 2.1.4

    Infers approximately-maximum-likelihood phylogenetic trees from
    alignments of nucleotide or protein sequences
    http://www.microbesonline.org/fasttree/

  281. FASTX-Toolkit
  282. module name: fastx
    version 0.0.14
    Other versions: 0.0.13, 0.0.13.2

    FASTQ/A short-reads pre-processing tools
    http://hannonlab.cshl.edu/fastx_toolkit/index.html
    Info: http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

    Depends on gcc
    Depends on perl
    Depends on libgtextutils

  283. FinisherSC
  284. module name: FinisherSC
    version 2.1

    FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
    https://github.com/kakitone/finishingTool
    https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv280

    Automatically loads MUMmer software; use "ml show MUMmer" to
    determine path which is needed to run finisherSC.py


    Depends on MUMmer
    Depends on biopython/2.7.12
    Depends on java/7

  285. FLASH (Fast Length Adjustment of SHort reads)
  286. module name: FLASH
    version 1.2.11
    Other versions: 1.2.10, 1.2.7, 1.2.8

    Merge mates from fragments that are shorter than twice the read length
    http://ccb.jhu.edu/software/FLASH/

    Depends on gcc

  287. flexbar
  288. module name: flexbar
    version 2.4

    Flexible barcode and adapter removal
    https://github.com/seqan/flexbar
    Info: /group/bioinfo/apps/apps/flexbar-2.4/README.txt

  289. Fold-Grammars
  290. module name: fold-grammars
    version 2014-03-17

    Components for dynamic programming problems covering RNA secondary structure predictions
    http://bibiwsserv.cebitec.uni-bielefeld.de/fold-grammars/
    Includes: pKiss and KnotInFrame
    http://bibiserv2.cebitec.uni-bielefeld.de/pkiss?id=pkiss_pkiss_manual_manual
    http://bibiserv2.cebitec.uni-bielefeld.de/knotinframe?id=knotinframe_manual_manual

    Depends on gapc

  291. FragGeneScan
  292. module name: FragGeneScan
    version 1.30
    Other versions: 1.16, 1.19

    Finds (fragmented) genes in short reads
    http://omics.informatics.indiana.edu/FragGeneScan/
    Example data in /group/bioinfo/apps/apps/FragGeneScan-1.30/example
    Training data in /group/bioinfo/apps/apps/FragGeneScan-1.30/train

    Depends on gcc

  293. FREEnc (FlExible Extraction of Long non-coding RNAs)
  294. module name: FEELnc
    version 2017-Oct-9

    Annotation pipeline for long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data
    https://github.com/tderrien/FEELnc

    Depends on perl
    Depends on R-bioconductor/3.4.0

  295. FusionCatcher
  296. module name: FusionCatcher
    version 0.99.6a
    Other versions: 0.99.4c, 0.99.5a, test

    Finder of somatic fusion-genes in RNA-seq data.
    https://github.com/ndaniel/fusioncatcher
    Manual: https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md

    For Ensembl data release 84

    You will need to use "fusioncatcher-build" command to create index files as described in the manual

    Depends on biopython/2.7.8
    Depends on bowtie/1.1.2
    Depends on STAR/2.5.1b
    Depends on bowtie2/2.2.9
    Depends on bwa/0.7.12
    Depends on seqtk/1.0-r82b
    Depends on velvet/1.2.10
    Depends on sra-toolkit/2.5.1
    Depends on samtools/0.1.19
    Depends on picard-tools/1.129
    Depends on parallel/20150522

  297. GAEMR (Genome Assembly Evaluation, Metrics and Reporting)
  298. module name: GAEMR
    version 1.0.1

    Report on a genome assembly's completeness, correctness, and contiguity
    http://www.broadinstitute.org/software/gaemr/
    Guide: http://www.broadinstitute.org/software/gaemr/users-guide/
    Manual: http://www.broadinstitute.org/software/gaemr/reference-manual/

    Depends on biopython/2.7.8
    Depends on bwa/0.7.12
    Depends on bowtie2/2.2.5
    Depends on blast/2.2.30+
    Depends on MUMmer/3.23
    Depends on rnammer/1.2
    Depends on samtools/0.1.18
    Depends on picard-tools/1.123
    Depends on rdp_classifier/2.4

  299. GAM-NGS
  300. module name: GAM-NGS
    version 1.1

    Genomic Assemblies Merger for NGS
    https://github.com/vice87/gam-ngs
    Example: /group/bioinfo/apps/apps/gam-ngs-1.1/example
    Ref: http://www.biomedcentral.com/1471-2105/14/S7/S6

    Depends on Boost
    Depends on bwa
    Depends on samtools/1.0

  301. GapCloser
  302. module name: GapCloser
    version 1.12-r6

    Close gaps which emerge from scaffolding process by SOAPdenovo or
    other assembler using the abundant pair relationships of short reads.
    http://soap.genomics.org.cn/soapdenovo.html
    Manual: /group/bioinfo/apps/apps/GapCloser-1.12-r6/GapCloser_Manual.pdf

    Depends on gcc

  303. GapFiller
  304. module name: GapFiller
    version 1.11

    Closing gaps within pre-assembled scaffold
    http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/
    Manual at /group/bioinfo/apps/apps/GapFiller-1.11/manual.pdf
    Tutorial at /group/bioinfo/apps/apps/GapFiller-1.11/tutorial.pdf
    License at /group/bioinfo/apps/apps/GapFiller-1.11/license.pdf

    Depends on gcc

  305. GATB-Core
  306. module name: gatb-core
    version 1.2.2

    Genome Analysis Toolbox with de-Bruijn graph
    https://gatb.inria.fr/software/gatb-core/
    http://gatb-core.gforge.inria.fr/doc/api/

    Depends on gcc
    Depends on cppunit/1.12.1

  307. GATK (Genome Analysis Toolkit; Full version)
  308. module name: GATK
    version 3.8.0
    Other versions: 2.2.15, 2.2.16, 2.3.0, 2.3.1, 2.3.3, 2.3.4, 2.3.5, 2.3.9, 2.4.3, 2.4.9, 2.5.2, 2.6.4, 2.6.5, 2.7.1, 2.7.2, 2.7.4, 2.8.1, 3.0.0, 3.1.1, 3.2.0, 3.2.2, 3.3.0, 3.4.0, 3.4.46, 3.5, 3.6.0, 3.7.0, 4.0.0.0, nightly-2015-08-23

    Analyse next-generation resequencing data
    http://www.broadinstitute.org/gatk/
    Forum: http://gatkforums.broadinstitute.org/
    Info: https://software.broadinstitute.org/gatk/documentation/quickstart
    GenomeAnalysisTK.jar file at /group/bioinfo/apps/apps/GATK-3.8.0
    Run the script "GenomeAnalysisTK" to use it.
    Or, use "java -jar $GATK -h", for example.
    License terms at /group/bioinfo/apps/apps/GATK-3.8.0/LICENSE
    Info: http://gatkforums.broadinstitute.org/discussion/6495/version-highlights-for-gatk-version-3-5

    Depends on java/8

  309. GATK Queue
  310. module name: GATK-Queue
    version 3.8.0
    Other versions: 3.2.2, 3.3.0, 3.4.0, 3.4.46, 3.5, 3.6

    Scripting framework for defining multi-stage genomic analysis pipelines
    http://gatkforums.broadinstitute.org/discussion/1306/overview-of-queue
    Queue.jar file at /group/bioinfo/apps/apps/GATK-Queue-3.8.0
    Run the script "Queue" to use it.
    License terms at /group/bioinfo/apps/apps/GATK-Queue-3.8.0/LICENSE

    Depends on GATK/3.8.0

  311. GATK-Lite (Genome Analysis Toolkit; Public version)
  312. module name: GATK-lite
    version lite-2.3.9
    Other versions: lite-2.2.13, lite-2.2.16, lite-2.3.0, lite-2.3.1, lite-2.3.4, lite-2.3.5

    Analyse next-generation resequencing data
    http://www.broadinstitute.org/gatk/
    Forum: http://gatkforums.broadinstitute.org/
    GenomeAnalysisTKLite.jar file at /group/bioinfo/apps/apps/GATK-lite-2.3.9
    Use "GenomeAnalysisTKLite" to use it.

    Depends on java

  313. GBS-SNP-CROP
  314. module name: GBS-SNP-CROP
    version 2.0

    GBS SNP Calling Reference Optional Pipeline
    https://github.com/halelab/GBS-SNP-CROP
    Manual: https://github.com/halelab/GBS-SNP-CROP/wiki
    Forum: https://groups.google.com/forum/#!forum/gbs-snp-crop
    Tutorial data available in /group/bioinfo/apps/apps/GBS-SNP-CROP-2.0/tutorial

    This probably does not work.

    Depends on pear/0.9.6
    Depends on java/8
    Depends on usearch/8.0.1623
    Depends on trimmomatic/0.33
    Depends on bwa/0.7.12
    Depends on samtools/1.2

  315. GDAL (Geospatial Data Abstraction Library)
  316. module name: GDAL
    version 2.2.1
    Other versions: 2.1.3

    Translator library for raster and vector geospatial data formats
    http://www.gdal.org/


    Depends on gcc
    Depends on biopython/2.7.12

  317. GEM (GEnome Multi-tool) Library
  318. module name: GEM
    version 20130406-045632
    Other versions: 1, 20130406-045632

    Next-generation sequence data handling tools
    http://big.crg.cat/services/gem_genome_multi_tool_library
    http://algorithms.cnag.cat/wiki/The_GEM_library
    Info in /group/bioinfo/apps/apps/GEM-20130406-045632-Intel/man

    Depends on gcc

  319. geneid
  320. module name: geneid
    version 1.4.4

    Predict genes in anonymous genomic sequences designed with a hierarchical structure
    http://genome.crg.es/software/geneid/
    Help: geneid -h

    Depends on gcc

  321. GeneMark-ES/ET
  322. module name: GeneMark
    version 4.32
    Other versions: 2.5m

    Gene Prediction in Eukaryotes
    http://exon.gatech.edu/GeneMark/

    Depends on perl

  323. Genepop
  324. module name: Genepop
    version 4.3
    Other versions: 4.1.4

    Population-genetics software for exact tests and ecumenicism
    http://kimura.univ-montp2.fr/~rousset/Genepop.htm
    Manual at http://kimura.univ-montp2.fr/%7Erousset/Genepop.pdf
    Manual at /group/bioinfo/apps/apps/Genepop-4.3/Genepop.pdf

    Depends on gcc

  325. GenePRIMP (Gene PRediction IMprovement Pipeline)
  326. module name: GenePRIMP
    version 0.3

    Identify & correct erroneous gene calls and missed genes
    http://geneprimp.jgi-psf.org/about.html
    Software license at /group/bioinfo/apps/apps/GenePRIMP-0.3/license.txt
    Info at /group/bioinfo/apps/apps/GenePRIMP-0.3/README

    Depends on blast/2.2.26

  327. GenomeMapper
  328. module name: GenomeMapper
    version 0.4.4

    Short read mapping tool designed for accurate read alignments
    http://1001genomes.org/software/genomemapper_singleref.html
    Manual:
    Manual: /group/bioinfo/apps/apps/genomemapper-0.4.4/doc/genomemapper_manual.pdf

  329. GenomeThreader
  330. module name: GenomeThreader
    version 1.6.5

    Compute gene structure predictions
    http://genomethreader.org/

    Depends on Vmatch/2.2.4

  331. GenomeTools
  332. module name: GenomeTools
    version 1.5.9
    Other versions: 1.3.9, 1.4.1, 1.5.8

    Bioinformatics tools collection including LTRharvest
    http://genometools.org/
    Manuals: /group/bioinfo/apps/apps/gt-1.5.9/doc

    LTRharvest: http://www.zbh.uni-hamburg.de/forschung/genominformatik/software/ltrharvest.html
    Manual: http://www.zbh.uni-hamburg.de/fileadmin/gi/LTRharvest/ltrharvestman.pdf

    Also includes gtfToGenePred to convert a GTF file to a genePred


    Depends on gcc

  333. Genovo
  334. module name: genovo
    version 0.4

    Metagenomic de novo Sequencing
    http://cs.stanford.edu/group/genovo/
    Manual: http://cs.stanford.edu/group/genovo/MANUAL
    Manual: /group/bioinfo/apps/apps/genovo-0.4/MANUAL

    Depends on gsl

  335. GFF3_to_GTF
  336. module name: GFF3_to_GTF
    version 1.0.0

    Converts data from GFF3 format to GTF format
    https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=afcb6456d8e300ed&tool_config=%2Fsrv%2Ftoolshed%2Fmain%2Fvar%2Fdata%2Frepos%2F000%2Frepo_21%2Ffml_gff_converter_programs%2Fgalaxy%2Fgff3_to_gtf.xml&changeset_revision=c6cf723c2ed4
    Info: /group/bioinfo/apps/apps/GFF3_to_GTF-1.0.0/README.md

    Depends on biopython/2.7.8

  337. gff3togtf
  338. module name: gff3togtf
    version 5c6f33e20fcc

    Tools for converting genome annotation between GTF, BED, GenBank and GFF
    https://github.com/vipints/GFFtools-GX/
    https://toolshed.g2.bx.psu.edu/repository?repository_id=afcb6456d8e300ed
    Info: /group/bioinfo/apps/apps/gff3togtf-5c6f33e20fcc/README.md

  339. gffcompare
  340. module name: gffcompare
    version 0.10.2

    Classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
    https://github.com/gpertea/gffcompare
    http://ccb.jhu.edu/software/stringtie/gff.shtml

  341. gffread
  342. module name: gffread
    version 0.9.10

    Validate, filter, convert and perform various other operations on GFF files
    https://github.com/gpertea/gffread
    http://ccb.jhu.edu/software/stringtie/gff.shtml

  343. GFOLD
  344. module name: gfold
    version 1.1.4

    Generalized fold change for ranking differentially expressed genes from RNA-seq data
    https://bitbucket.org/feeldead/gfold/
    Info: man gfold
    Info: http://compbio.tongji.edu.cn/~fengjx/GFOLD/gfold.html

    Depends on gsl/1.15

  345. Glasgow Haskell Compiler
  346. module name: ghc
    version 6.12.3
    Other versions: 7.6.3

    Compiler and interactive environment for the functional language Haskell
    http://www.haskell.org/ghc/
    http://www.haskell.org/ghc/download_ghc_6_12_3
    Info: /group/bioinfo/apps/apps/ghc-6.12.3/share/doc/ghc
    man ghc


    Depends on gcc

  347. GLIMMER
  348. module name: Glimmer
    version 3.02

    GLIMMER (Gene Locator and Interpolated Markov ModelER) is a system for finding genes in microbial DNA
    http://www.cbcb.umd.edu/software/glimmer/
    Manual: http://www.cbcb.umd.edu/software/glimmer/glim302notes.pdf

    Depends on gcc

  349. GlimmerHMM
  350. module name: GlimmerHMM
    version 3.0.1

    Gene finder based on a Generalized Hidden Markov Model (GHMM)
    http://www.cbcb.umd.edu/software/GlimmerHMM/
    Manual: http://www.cbcb.umd.edu/software/GlimmerHMM/man.shtml

  351. GMAP and GSNAP
  352. module name: gmap
    version 2016-05-01
    Other versions: 2012-01-11, 2012-04-27, 2012-11-27, 2014-02-20, 2014-12-16v2, 2014-12-16v2-amd, 2014-12-21-amd, 2017-01-14, 2017-01-14-mpi

    A Genomic Mapping and Alignment Program for mRNA and EST Sequences
    http://research-pub.gene.com/gmap/
    Manual: http://research-pub.gene.com/gmap/src/README
    Manual: /group/bioinfo/apps/apps/gmap-2016-05-01/README

    No genome databases for GMAP and GSNAP are installed. You can
    build your own or download prebuilt ones from the web site.

    Depends on gcc
    Depends on perl/5.20.1
    Depends on zlib
    Depends on bzip2

  353. GMcloser
  354. module name: GMcloser
    version 1.6
    Other versions: 1.5.1

    Closing the gaps in scaffolds with preassembled contigs
    https://sourceforge.net/projects/gmcloser/
    Manual: /group/bioinfo/apps/apps/GMcloser-1.6/Manual_GMcloser.pdf

    Includes gmvalue version 1.2

    Depends on MUMmer/3.23
    Depends on blast
    Depends on perl
    Depends on bowtie2
    Depends on yass

  355. GMP
  356. module name: gmp
    version 5.0.4
    Other versions: 5.0.3

    GNU MP Bignum Library
    http://gmplib.org/
    Manual: http://gmplib.org/manual/

    Depends on gcc

  357. GMvalue
  358. module name: GMvalue
    version 1.3

    Create genomic sequence assembly and evaluate its accuracy
    https://sourceforge.net/projects/gmcloser/
    Manual: /group/bioinfo/apps/apps/GMvalue-1.3/Manual_GMvalue.pdf

    Depends on MUMmer/3.23
    Depends on perl

  359. GNU Autoconf
  360. module name: autoconf
    version 2.69

    M4 macros to make shell scripts to configure software
    http://www.gnu.org/software/autoconf/

    Depends on m4

  361. GNU Automake
  362. module name: automake
    version 1.14

    Automatically generate Makefile.in
    http://www.gnu.org/software/automake/

    Depends on autoconf

  363. GNU Libtool
  364. module name: libtool
    version 2.4.2

    Generic library support script
    https://www.gnu.org/software/libtool/

  365. GNU M4
  366. module name: m4
    version 1.4.17

    Unix macro processor
    http://www.gnu.org/software/m4/

  367. GNU MPFR
  368. module name: mpfr
    version 3.1.2

    Library for multiple-precision floating-point computations with correct rounding
    http://www.mpfr.org/

    Depends on gcc
    Depends on gmp

  369. GNU parallel
  370. module name: parallel
    version 20170722
    Other versions: 20130122, 20130722, 20150522, 20150622

    Shell tool for executing jobs in parallel
    http://www.gnu.org/software/parallel/
    Manual: http://www.gnu.org/software/parallel/man.html
    Manual: use "man parallel"
    Also man pages for niceload, sem and sql

  371. GNU Scientific Library (GSL)
  372. module name: gsl
    version 2.3
    Other versions: 1.15

    Numerical library for C and C++ programmers
    http://www.gnu.org/software/gsl/
    Manual: http://www.gnu.org/software/gsl/manual/html_node/
    man -s3 gsl


    Depends on gcc

  373. GNU Texinfo
  374. module name: texinfo
    version 6.5

    The GNU Documentation System
    https://www.gnu.org/software/texinfo/

    Depends on gcc

  375. Gnuplot
  376. module name: gnuplot
    version 4.6.6
    Other versions: 4.6.1, 4.6.2, 5.0.5

    Portable, command-line driven graphing utility
    http://www.gnuplot.info/
    Manual: man gnuplot
    Manual: /group/bioinfo/apps/apps/gnuplot-4.6.6/gnuplot.pdf
    Manual: http://www.gnuplot.info/documentation.html
    FAQ: /group/bioinfo/apps/apps/gnuplot-4.6.6/FAQ.pdf
    FAQ: http://www.gnuplot.info/faq/index.html

    Depends on gcc

  377. gpg-error
  378. module name: libgpg-error
    version 1.12

    Library with error codes and descriptions shared by most GnuPG related software
    http://www.gnupg.org/related_software/libgpg-error/index.en.html
    http://www.gnupg.org/download/

    Depends on gcc

  379. GraPhlAn
  380. module name: graphlan
    version 2017-01-21

    Make circular representations of taxonomic and phylogenetic trees
    https://bitbucket.org/nsegata/graphlan/wiki/Home
    Example data: /group/bioinfo/apps/apps/GraPhlAn-2017-01-21/examples


    Depends on biopython/2.7.12

  381. Graphviz
  382. module name: graphviz
    version 2.38.0

    Graph Visualization Software
    http://www.graphviz.org/
    Documentation: http://www.graphviz.org/Documentation.php
    Documentation: /group/bioinfo/apps/apps/graphviz-2.38.0/share/graphviz/doc/html/index.html

    Depends on gcc

  383. GREAT (Genomic Regions Enrichment of Annotations Tool)
  384. module name: GREAT
    version 1.2

    Predicts functions of cis-regulatory regions
    http://bejerano.stanford.edu/help/display/GREAT/Home
    Forum: http://bejerano.stanford.edu/forum
    Manual: /group/bioinfo/apps/apps/greatTools-1.2/README.txt

    Includes the core calculation engine tools:
    - createRegulatoryDomains to calculate regulatory domains
    - calculateBinomialP to calculate genomic region-based binomial p-values

    Depends on gcc

  385. GrooopM
  386. module name: GroopM
    version 0.3.4

    Metagenomic binning suite
    https://github.com/ecogenomics/GroopM
    http://ecogenomics.github.io/GroopM/
    Manual: http://ecogenomics.github.io/GroopM/manual/GroopM_manual.pdf


    Depends on biopython/2.7.12
    Depends on BamM
    Depends on numexpr

  387. GS FLX
  388. module name: 454
    version 2.9
    Other versions: 2.6, 2.7, 2.8

    Roche 454 Sequencing System Software
    http://www.454.com/
    Manuals in /group/bioinfo/apps/apps/454-2.9/doc

    Depends on gcc
    Depends on java/6

  389. gstreamer
  390. module name: gstreamer
    https://gstreamer.freedesktop.org/
    Open source multimedia framework
    Includes plugins-base

    Depends on gcc

  391. gtextutils
  392. module name: libgtextutils
    version 0.7
    Other versions: 0.6

    GNU Text Utilities
    http://www.gnu.org/software/textutils/textutils.html

    Depends on gcc

  393. gVCFtools
  394. module name: gvcftools
    version 0.15

    Tools to create and analyze gVCF files
    https://sites.google.com/site/gvcftools/home

    Depends on gcc

  395. HALC
  396. module name: HALC
    version 2017-09-06

    High Throughput Algorithm for Long Read Error Correction
    https://github.com/lanl001/halc
    Info: /group/bioinfo/apps/apps/HALC-2017-09-06/Readme.md

    Depends on blasr
    Depends on LoRDEC

  397. HAllA: Hierarchical All-against-All significance testing
  398. module name: halla
    version 0.6.3

    Statistical method for discovery of significant relationships among data features with high power.
    Python module
    http://huttenhower.sph.harvard.edu/halla
    Forum: https://groups.google.com/forum/#!forum/halla-users

    Depends on biopython/2.7.11

  399. hapsembler
  400. module name: hapsembler
    version 2.21

    Haplotype-specific genome assembly toolkit
    Designed for genomes that are rich in SNPs and other types of polymorphism
    http://compbio.cs.toronto.edu/hapsembler/
    Manual: /group/bioinfo/apps/apps/hapsembler-2.21/doc/hapsembler-2.21_manual.pdf

    Depends on gcc

  401. Haskell Platform
  402. module name: haskell-platform
    version 2013.2.0.0-ghc-7.6.3

    Environment for the functional language Haskell
    http://www.haskell.org/platform/

    Depends on ghc/7.6.3

  403. HDF5
  404. module name: HDF5
    version 1.8.19
    Other versions: 1.8.14

    Data model, library, and file format for storing and managing data
    Clustering de novo assembled transcripts and counting overlapping reads
    http://www.hdfgroup.org/HDF5/

  405. HGTector
  406. module name: HGTector
    version 0.2.1

    Genome-wide prediction of horizontal gene transfer events based on Blast hit distribution statistics
    https://github.com/DittmarLab/HGTector

    Feb 4 2017 release

    Depends on perl
    Depends on R-bioconductor/3.3.0

  407. HISAT2
  408. module name: hisat2
    version 2.0.5
    Other versions: 2.0.4

    Graph-based alignment of next generation sequencing reads to a population of genomes
    http://ccb.jhu.edu/software/hisat2/index.shtml
    Manual: http://ccb.jhu.edu/software/hisat2/manual.shtml
    FAQ: http://ccb.jhu.edu/software/hisat2/faq.shtml

    Depends on gcc

  409. HMMER
  410. module name: HMMER
    version 3.1b2
    Other versions: 2.3.2, 3.0, 3.1, 3.1b1

    Biosequence analysis using profile hidden Markov models
    http://hmmer.janelia.org/
    Help: http://hmmer.janelia.org/help
    Manual: /group/bioinfo/apps/apps/hmmer-3.1b2/Userguide.pdf
    Info: /group/bioinfo/apps/apps/hmmer-3.1b2/release-notes


    Depends on gcc

  411. HOMER (Hypergeometric Optimization of Motif EnRichment)
  412. module name: HOMER
    version 4.9
    Other versions: 4.1, 4.3, 4.7, 4.7b

    Suite of tools for Motif Discovery and next-gen sequencing analysis
    http://homer.salk.edu/homer/
    Manual: /group/bioinfo/apps/apps/HOMER-4.9/DoughnutDocumentation.pdf

    Installed data:
    ORGANISMS
    + fly-o v5.10 Drosophila melanogaster (fly) accession and ontology information
    + mouse-o v5.10 Mus musculus (mouse) accession and ontology information
    + human-o v5.10 Homo sapiens (human) accession and ontology information
    + arabidopsis-o v5.10 Arabidopsis thaliana (arabidopsis) accession and ontology information
    PROMOTERS
    + arabidopsis-p v5.0 Arabidopsis Ensembl Promoters (tair10)
    + human-p v5.5 human promoters (human)
    + fly-p v5.5 fly promoters (fly)
    GENOMES
    + tair10 v5.10 arabidopsis genome and annotation (tair10)
    + mm10 v5.10 mouse genome and annotation for UCSC mm10
    + hg38 v5.10 human genome and annotation for UCSC hg38
    + hg19 v5.10 human genome and annotation for UCSC hg19


    Depends on perl
    Depends on samtools
    Depends on R

  413. HTSeq
  414. module name: htseq
    version 0.7.0
    Other versions: 0.5.3p3, 0.6.1

    Analysing high-throughput sequencing data with Python
    https://github.com/simon-anders/htseq


    Depends on biopython/2.7.12

  415. htslib
  416. module name: htslib
    version 1.6
    Other versions: 1.3, 1.3.1, 1.3.2, 1.4, 1.5

    A C library for reading/writing high-throughput sequencing data
    http://www.htslib.org/
    Includes these programs: bgzip, htsfile, tabix
    man pages for: htsfile, tabix, sam, faidx, vcf

    Depends on perl
    Depends on curl
    Depends on xz

  417. HUMAnN2: The HMP Unified Metabolic Analysis Network 2
  418. module name: humann2
    version 0.11.1
    Other versions: 0.10.0

    Pipeline for profiling microbial pathways from sequencing data
    http://huttenhower.sph.harvard.edu/humann2
    Changes: /group/bioinfo/apps/apps/humann2-0.11.1/history.md

    Includes full databases from:
    http://huttenhower.sph.harvard.edu/humann2_data/chocophlan/full_chocophlan_plus_viral.v0.1.1.tar.gz
    http://huttenhower.sph.harvard.edu/humann2_data/uniprot/uniref_annotated/uniref90_annotated_1_1.tar.gz

    Forum: https://groups.google.com/forum/#!forum/humann-users
    Manual: http://huttenhower.sph.harvard.edu/humann2/manual
    Tutorial: https://bitbucket.org/biobakery/biobakery/wiki/humann2

    Depends on metaphlan2
    Depends on diamond
    Depends on MinPath
    Depends on RAPsearch
    Depends on usearch/8

  419. HUMAnN: The HMP Unified Metabolic Analysis Network
  420. module name: humann
    version 0.99

    Pipeline for measuring microbial pathways in metagenomic data
    https://huttenhower.sph.harvard.edu/humann

    Need to copy files into your own space before running:
    $ cd $RCAC_SCRATCH
    $ tar zxf $HUMANN_PKG
    $ cd humann-0.99
    $ less README.text # start reading at "INPUTS" section


    Depends on biopython/2.7.12
    Depends on blast
    Depends on R-bioconductor/3.3.0
    Depends on MinPath
    Depends on maq

  421. hyb
  422. module name: hyb
    version Nov2014

    Pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data
    https://github.com/gkudla/hyb
    Info: man hyb

    Depends on blat
    Depends on flexbar
    Depends on blast
    Depends on bowtie2
    Depends on ViennaRNA
    Depends on unafold

  423. i-ADHoRe
  424. module name: i-adhore
    version 3.0.01-mpi-b
    Other versions: 3.0.01, 3.0.01-mpi

    Detect degenerated homology relations within and between different genomes
    http://bioinformatics.psb.ugent.be/software/details/i--ADHoRe
    Manual: /group/bioinfo/apps/apps/i-adhore-3.0.01-mpi-b/documentation/iADHoRe_manual_3_0.pdf
    Includes support for MPI

    Depends on gcc
    Depends on openmpi

  425. IDBA
  426. module name: idba
    version 1.1.2
    Other versions: 0.19, 1.1.0, 1.1.1, 1.1.3

    Iterative De Bruijn Graph De Novo short read assembler specially
    designed with highly uneven sequencing depth
    http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/index.html
    https://github.com/loneknightpy/idba
    IDBA, IDBA-UD, IDBA-Hybrid and IDBA-Tran all in one package

    Depends on gcc
    Depends on blat

  427. IDBA-UD
  428. module name: idba_ud
    version 1.0.9

    Iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing
    data with Highly Uneven Sequencing Depth.
    http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/index.html

    Depends on biopython/2.7.2

  429. IDR (Irreproducible Discovery Rate)
  430. module name: idr
    version 2.0.3

    Measures consistency between replicates in high-throughput experiments
    https://www.encodeproject.org/software/idr/
    https://sites.google.com/site/anshulkundaje/projects/idr
    Version info: https://groups.google.com/forum/#!topic/idr-discuss/A7PaMnzoFwg

    Depends on biopython/3.5.1

  431. igraph
  432. module name: igraph
    version 0.7.1

    The network analysis package
    http://igraph.org/c/

    Depends on gcc

  433. IGV (Integrative Genomics Viewer)
  434. module name: igv
    version 2.3.60
    Other versions: 2.1.13, 2.1.30, 2.3.12, 2.3.57

    Visualization tool for interactive exploration of genomic datasets
    http://www.broadinstitute.org/software/igv/home
    User Guide: http://www.broadinstitute.org/software/igv/UserGuide
    FAQ: http://www.broadinstitute.org/software/igv/FAQ
    Forum: https://groups.google.com/forum/#!forum/igv-help
    Info: /group/bioinfo/apps/apps/IGV_2.3.60/readme.txt
    Start with "igv.sh"
    Need X11 display: More config info at:
    https://www.rcac.purdue.edu/compute/carter/guide/#accounts_login_x11

    Depends on java

  435. IGV Tools
  436. module name: igvtools
    version 2.3.60
    Other versions: 2.1.24, 2.1.7, 2.3.12, 2.3.57

    Utilities for preprocessing data files
    http://www.broadinstitute.org/software/igv/home
    User Guide: http://www.broadinstitute.org/software/igv/UserGuide
    FAQ: http://www.broadinstitute.org/software/igv/FAQ
    Forum: https://groups.google.com/forum/#!forum/igv-help
    Info: /group/bioinfo/apps/apps/IGVTools-2.3.60/igvtools_readme.txt
    Need X11 display for igvtools_gui

    Depends on java

  437. IMAGE
  438. module name: image
    version 2.33
    Other versions: 2.31

    Iterative Mapping and Assembly for Gap Elimination
    Close gaps in any draft assembly using Illumina paired end reads
    http://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page
    Manual at http://sourceforge.net/apps/mediawiki/image2/index.php?title=How_to_run_IMAGE
    Note: This software doesn't work

    Depends on gcc

  439. ImageMagick
  440. module name: ImageMagick
    version 6.8.6-8
    Other versions: 6.8.9-8

    Software suite to create, edit, compose, or convert bitmap images
    http://www.imagemagick.org/script/index.php

    Depends on gcc

  441. indelMINER
  442. module name: indelMINER
    version 1.0

    Identify indels in whole-genome resequencing project
    http://www.biomedcentral.com/1471-2105/16/42

    Depends on gcc

  443. Infernal ("INFERence of RNA ALignment")
  444. module name: infernal
    version 1.1.2
    Other versions: 1.0.2, 1.1.1

    Builds probabilistic profiles of the sequence and secondary structure of an RNA family
    http://eddylab.org/infernal/
    Manual: /group/bioinfo/apps/apps/infernal-1.1.2-linux-intel-gcc/Userguide.pdf
    Inf: /group/bioinfo/apps/apps/infernal-1.1.2-linux-intel-gcc/documentation/
    Ref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810854/


    Depends on gcc

  445. InParanoid
  446. module name: InParanoid
    version 4.1

    Identify orthologs
    http://inparanoid.sbc.su.se/cgi-bin/index.cgi

    Need to make copy of InParanoid files to your own directory and run from there.
    For example:
    cd $RCAC_SCRATCH
    tar zxf $INPARANOID
    cd inparanoid-4.1
    # consult README file on how to use software


    Depends on perl
    Depends on java
    Depends on blast/2.2.26

  447. iNPS
  448. module name: iNPS
    version 1.0

    Accurate nucleosome positioning from sequencing data
    http://www.picb.ac.cn/hanlab/iNPS.html
    Manual: /group/bioinfo/apps/apps/iNPS_V1.0/iNPS_1.0_User_manual.pdf

    Depends on python/3.4.1

  449. InterProScan
  450. module name: InterProScan
    version 5.27-66.0
    Other versions: 5.10-50.0, 5.11-51.0, 5.12-52.0, 5.13-52.0, 5.1-44.0, 5.14-53.0, 5.15-54.0, 5.16-55.0, 5.17-56.0, 5.18-57.0, 5.19-58.0, 5.20-59.0, 5.21-60.0, 5.22-61.0, 5.23-62.0, 5.2-45.0, 5.24-63.0, 5.25-64.0, 5.26-65.0, 5.3-46.0, 5.4-47.0, 5.5-48.0, 5.6-48.0, 5.7-48.0, 5.8-49.0, 5.9-50.0, 5-RC7

    Scans a range of protein signatures against your sequence
    https://github.com/ebi-pf-team/interproscan/wiki
    Manual: https://github.com/ebi-pf-team/interproscan/wiki/HowToRun

    Notes: https://github.com/ebi-pf-team/interproscan/wiki/Interproscan5_27_66_ReleaseNotes
    InterPro version 66.0 data (includes Panther 12 data)
    Uses pre-calculated match lookup service at http://www.ebi.ac.uk
    Includes support for TMHMM, Phobius and SignalP

    To adjust parameters in interproscan.properties file, you need to copy
    the software and run it in your own directory. See instructions at
    /group/bioinfo/apps/apps/interproscan-5.27-66.0/README.local

    Depends on perl
    Depends on biopython/2.7.8
    Depends on java/8
    Depends on signalp
    Depends on tmhmm
    Depends on phobius

  451. IPknot
  452. module name: ipknot
    version 0.0.2

    RNA pseudoknot prediction based on maximizing expected accuracy
    http://www.ncrna.org/software/ipknot/
    Info: /group/bioinfo/apps/apps/ipknot-0.0.2/README.rd

  453. iPlant iRODS iCommands
  454. module name: icommands
    version 3.0

    Storing and accessing iPlant data with iRODS
    https://pods.iplantcollaborative.org/wiki/display/start/Storing+Your+Data+with+iPlant+and+Accessing+that+Data
    https://pods.iplantcollaborative.org/wiki/display/start/Using+icommands
    https://pods.iplantcollaborative.org/wiki/display/start/Sharing+Your+Data
    https://www.irods.org/index.php/What_is_iRODS%3F

  455. IQ-TREE
  456. module name: IQ-TREE
    version 1.5.5

    Infer phylogenetic trees by maximum likelihood
    http://www.iqtree.org/
    https://github.com/Cibiv/IQ-TREE
    Manual: http://www.iqtree.org/doc/
    Includes both iqtree and iqtree-omp

  457. Isaac Aligner
  458. module name: isaac_aligner
    version 01.13.06.27

    Illumina/HiSeq Human WGS analysis workflow
    https://github.com/sequencing/isaac_aligner
    http://blog.basespace.illumina.com/2013/06/04/introducing-fast-free-alignment-and-variant-calling-with-the-isaac-human-whole-genome-sequencing-app/
    License: /group/bioinfo/apps/apps/issac_aligner-01.13.06.27/Illumina_Open_Source_License_1.pdf

    Depends on gcc
    Depends on gnuplot

  459. Isaac Variant Caller
  460. module name: isaac_variant_caller
    version 1.0.4

    Detect SNVs and small indels from the aligned sequencing reads of a single
    diploid sample.
    https://github.com/sequencing/isaac_variant_caller
    License: /group/bioinfo/apps/apps/isaac_variant_caller-1.0.4/Illumina_Open_Source_License_1.pdf

    Depends on gcc
    Depends on gvcftools

  461. ITSx
  462. module name: ITSx
    version 1.0.11

    Extract ITS1 and ITS2 (fungal molecular barcode) subregions from ITS sequences.
    http://microbiology.se/software/itsx/
    Manual: /group/bioinfo/apps/apps/ITSx_1.0.11/manual.pdf
    Manual: http://microbiology.se/publ/itsx_users_guide.pdf

    Depends on HMMER

  463. jabba
  464. module name: jabba
    version 1.0.0

    Read error correction tool for PacBio data
    https://github.com/biointec/jabba
    Info: https://github.com/biointec/jabba/wiki

    Depends on gcc

  465. Java
  466. module name: java
    version 1.8.0_161
    Other versions: 1.6.0_31, 1.6.0_38, 1.6.0_39, 1.6.0_43, 1.6.0_45, 1.7.0_04, 1.7.0_05, 1.7.0_07, 1.7.0_09, 1.7.0_10, 1.7.0_11, 1.7.0_13, 1.7.0_17, 1.7.0_21, 1.7.0_25, 1.7.0_40, 1.7.0_45, 1.7.0_51, 1.7.0_55, 1.7.0_67, 1.7.0_71, 1.7.0_75, 1.7.0_79, 1.8.0, 1.8.0_05, 1.8.0_101, 1.8.0_11, 1.8.0_111, 1.8.0_121, 1.8.0_131, 1.8.0_144, 1.8.0_151, 1.8.0_20, 1.8.0_25, 1.8.0_31, 1.8.0_45, 1.8.0_60, 1.8.0_65, 1.8.0_73, 1.8.0_77, 1.8.0_91, 6, 7, 8, 9, 9.0.1, 9.0.4

    Java Standard Edition Development Kit (JDK) for Linux on Intel 64 machines
    http://www.oracle.com/technetwork/java/javase/downloads/index.html
    Critical Patch Update (CPU) release--fixes vulnerabilities and critical bugs

  467. Jellyfish
  468. module name: jellyfish
    version 2.2.6
    Other versions: 1.1.11, 1.1.3, 1.1.4, 2.1.1, 2.2.4

    Fast, Parallel k-mer Counting for DNA
    https://github.com/gmarcais/Jellyfish
    http://www.genome.umd.edu/jellyfish.html
    Manual: "man jellyfish"
    Manual: ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf

    Depends on gcc

  469. jemalloc
  470. module name: jemalloc
    version 3.4.1

    Memory allocator with fragmentation avoidance and scalable concurrency support
    http://www.canonware.com/jemalloc/index.html
    man -s3 jemalloc

    Depends on gcc

  471. JIGSAW:
  472. module name: jigsaw
    version 3.2.10

    Gene prediction using multiple sources of evidence
    http://cbcb.umd.edu/software/jigsaw/
    Info in /group/bioinfo/apps/apps/jigsaw-3.2.10/README.txt

    Depends on gcc
    Depends on perl

  473. jModelTest
  474. module name: jModelTest
    version 2.1.4

    Statistical selection of best-fit models of nucleotide substitution
    http://code.google.com/p/jmodeltest2/
    Manual: http://code.google.com/p/jmodeltest2/wiki/GettingStarted

    Run as: java -jar $JMODELTEST_HOME/jModelTest.jar ...

    May need to copy to your home directory in order to run:
    cp -r $JMODELTEST_HOME ~/.
    cd jModelTest-2.1.4
    [modify conf/jmodeltest.conf as needed]
    java -jar jModelTest.jar ...

    Need X11 support to run GUI

    Depends on java
    Depends on phyml

  475. KAAS - KEGG Automatic Annotation Server
  476. module name: KAAS
    version 2.0

    Functional annotation of genes by BLAST comparisons against the
    manually curated KEGG GENES database
    http://www.genome.jp/tools/kaas/
    To use: review instructions at /group/bioinfo/apps/apps/KAAS-2.0/readme.txt
    Then, copy /group/bioinfo/apps/apps/KAAS-2.0/kaas.config to your working directory
    Issue all KAAS commands from that directory

    Depends on ruby
    Depends on perl
    Depends on HMMER
    Depends on blast/2.2.26

  477. kallisto
  478. module name: kallisto
    version 0.43.1
    Other versions: 0.43.0

    Quantify abundances of transcripts from RNA-Seq data
    https://pachterlab.github.io/kallisto/
    Manual: https://pachterlab.github.io/kallisto/manual
    Ref: http://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html

    Depends on gcc

  479. KARECT (KAUST Assembly Read Error Correction Tool)
  480. module name: karect
    version 1.0

    Correction of Substitution, Insertion and Deletion Errors for Next-generation Sequencing Data
    https://github.com/aminallam/karect
    http://aminallam.github.io/karect/

    Depends on gcc

  481. kentUtils
  482. module name: kentUtils
    version 302.1.0

    UCSC command line bioinformatic utilities
    http://genome.cse.ucsc.edu/index.html
    https://github.com/ENCODE-DCC/kentUtils

    Depends on gcc

  483. khmer
  484. module name: khmer
    version 1.4.1
    Other versions: 2012-07-06

    In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
    http://khmer.readthedocs.org/en/v1.4.1/
    Forum: http://lists.idyll.org/listinfo/khmer
    Info in /group/bioinfo/apps/apps/khmer-1.4.1/doc
    Citation: /group/bioinfo/apps/apps/khmer-1.4.1/CITATION

    Depends on gcc
    Depends on tcl
    Depends on igraph
    Depends on HDF5/1.8.14
    Depends on R-bioconductor/3.1.0

  485. KmerGenie
  486. module name: kmergenie
    version 1.6982
    Other versions: 1.5692

    Estimates the best k-mer length for de novo assembly
    http://kmergenie.bx.psu.edu/

    Built with maximum kmer size = 200

    Depends on biopython/2.7.8

  487. KOBAS (KEGG Orthology Based Annotation System).
  488. module name: KOBAS
    version 2.1.0


    Identify statistically significantly enriched pathways, human
    diseases, and functional terms for an input set of genes using
    biological knowledge from well-known pathway databases, disease
    databases, and Gene Ontology.

    http://kobas.cbi.pku.edu.cn/home.do
    Tutorial: http://kobas.cbi.pku.edu.cn/help.do
    Tutorial: /group/bioinfo/apps/apps/kobas-2.1.0/doc/tutorial.txt
    Release notes: /group/bioinfo/apps/apps/kobas-2.1.0/doc/Release_Note.txt

    Depends on biopython/2.7.8
    Depends on blast

  489. kSNP
  490. module name: meraculous
    version 2.0.5

    Distributed and scalable assembler for eukaryotic genomes
    http://jgi.doe.gov/data-and-tools/meraculous/
    Manual: /group/bioinfo/apps/apps/meraculous-2.0.5/share/doc/meraculous/Manual.pdf

    Depends on gcc
    Depends on Boost
    Depends on perl

  491. L_RNA_scaffolder
  492. module name: L_RNA_scaffolder
    version 14Feb2014

    Long transcriptome reads to scaffold genome
    http://www.fishbrowser.org/software/L_RNA_scaffolder/index.php?action=isin
    Manual: http://www.fishbrowser.org/software/L_RNA_scaffolder/index.php?action=isin&do=documentation

    Depends on gcc
    Depends on perl/5.18.1

  493. LAPACK Linear Algebra PACKage and BLAS
  494. module name: lapack
    version 3.4.2

    http://www.netlib.org/lapack/
    compiled with gcc 4.7.2

    Depends on gcc

  495. LAST
  496. module name: LAST
    version 801

    Finds similar regions between sequences
    http://last.cbrc.jp/

    Depends on gcc

  497. LASTZ
  498. module name: LASTZ
    version 1.04.00

    Pairwise DNA sequence aligner
    https://github.com/lastz/lastz
    http://www.bx.psu.edu/~rsharris/lastz/
    Manual: http://www.bx.psu.edu/~rsharris/lastz/README.lastz-1.04.00.html

    Includes lastz_32


    Depends on biopython/2.7.12

  499. LEfSe: (Linear discriminant analysis effect size)
  500. module name: lefse
    version 2017-02-03

    Find biomarkers between two or more groups using relative abundances
    Info in step #4 in https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial
    Tutorial: https://bitbucket.org/biobakery/biobakery/wiki/lefse
    Run it online: https://huttenhower.sph.harvard.edu/galaxy/


    Depends on biopython/2.7.12
    Depends on R-bioconductor/3.3.0

  501. libcfu
  502. module name: libcfu
    version 0.03

    Multithreaded software library
    https://sourceforge.net/projects/libcfu/

    Depends on gcc

  503. libgcrypt
  504. module name: libgcrypt
    version 1.5.3

    General purpose cryptographic library
    http://www.gnu.org/software/libgcrypt/

    Depends on libgpg-error

  505. libsvm
  506. module name: libsvm
    version 322

    Support vector classification, regression and distribution estimation.
    http://www.csie.ntu.edu.tw/~cjlin/libsvm/index.html
    https://github.com/cjlin1/libsvm

    Depends on gcc

  507. libuuid
  508. module name: libuuid
    version 2.17.0

    Universally Unique ID library
    Libs in /group/bioinfo/apps/apps/libuuid-2.17.0/lib64
    Header/include files in/group/bioinfo/apps/apps/libuuid-2.17.0/include

    Depends on gcc

  509. libxml2
  510. module name: libxml2
    version 2.9.1

    XML C parser and toolkit developed for the Gnome project
    http://www.xmlsoft.org/

    Depends on gcc

  511. libxslt
  512. module name: libxslt
    version 1.1.28

    XSLT C library developed for the GNOME project
    XSLT is a an XML language to define transformation for XML
    http://xmlsoft.org/XSLT/

    Depends on gcc
    Depends on libxml2

  513. lmstat
  514. module name: lmstat
    version 11.11.0.0

    Report status on license manager daemons and feature usage
    https://www.flexera.com/producer/support/top-support-resources/
    Example: lmstat -a -c port@license.server.domain.name

  515. lncRNA-screen
  516. module name: lncRNA-screen
    version 0.1

    Pipeline for computationally screening putative lncRNA transcripts over multimodal datasets
    https://github.com/NYU-BFX/lncRNA-screen

    Warning: this probably does not work.

    First, put a copy of the program files somewhere you can manage:

    $ cd $RCAC_SCRATCH
    $ cp -r /group/bioinfo/apps/apps/lncRNA-screen-0.1 ./.
    $ cd lncRNA-screen-0.1/lncRNA-screen

    Next, follow the directions in the "Setting up" section of the web
    site for where to put your data and hints on how to run.


    Depends on biopython/2.7.11
    Depends on samtools/0.1.19
    Depends on R-bioconductor/3.3.0

  517. lncRScan-SVM
  518. module name: lncRScan-SVM
    version 1.0.1

    Predict long non-coding RNAs (lncRNAs) or protein coding transcripts using a support vector machine (SVM)
    https://sourceforge.net/projects/lncrscansvm/files/

    Need to run from your own directory.
    Use "setup_lncRScan-SVM $RCAC_SCRATCH" to run from your scratch directory

    Depends on biopython/2.7.11
    Depends on libsvm

  519. LoRDEC
  520. module name: LoRDEC
    version 0.5.3

    A hybrid error correction program for long, PacBio reads
    https://gatb.inria.fr/software/lordec/
    http://atgc.lirmm.fr/lordec/
    Warning: This software might not work

    Depends on gcc

  521. LoRMA
  522. module name: LoRMA
    version 0.4

    Correct sequencing errors in long reads
    https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/
    Warning: This software might not work

    Depends on gcc
    Depends on LoRDEC

  523. LTR_FINDER
  524. module name: LTR_FINDER
    version 1.0.6
    Other versions: 1.0.5

    Find full-length LTR retrotransposons in genome sequences
    http://tlife.fudan.edu.cn/ltr_finder/
    Info: /group/bioinfo/apps/apps/LTR_FINDER.x86_64-1.0.6/help.pdf

    Depends on gcc

  525. Lucy
  526. module name: lucy
    version 1.20p

    DNA sequence quality and vector trimming tool
    http://lucy.sourceforge.net/
    Manual: man lucy

    Depends on gcc

  527. lz4
  528. module name: lz4
    version 131
    Other versions: 122

    Extremely Fast Compression algorithm
    https://github.com/Cyan4973/lz4
    http://fastcompression.blogspot.com/p/lz4.html
    man lz4

    Depends on gcc

  529. MACS
  530. module name: macs
    version 2.1.0.20150420
    Other versions: 1.4.2a, 1.4.2b, 2.0.10, 2.0.10-2.7.2, 2.1.0

    Model-based Analysis for ChIP-Seq
    https://github.com/taoliu/MACS/
    Info: /group/bioinfo/apps/apps/MACS-2.1.0.20150420/README.rst

    Depends on biopython/2.7.12

  531. MAFFT
  532. module name: mafft
    version 6.903

    Multiple alignment program for amino acid or nucleotide sequences
    http://mafft.cbrc.jp/alignment/server/index.html
    man pages for mafft and mafft-homologs

  533. MAGeCK-VISPR
  534. module name: MAGeCK-VISPR
    version 0.5.3

    Quality control, analysis and visualization workflow for CRISPR/Cas9 screens
    https://bitbucket.org/liulab/mageck-vispr/overview



  535. MAKER
  536. module name: MAKER
    version 2.31.9-nompi
    Other versions: 2.10, 2.27b, 2.28b, 2.28b-rev2, 2.30p, 2.31.7, 2.31.8, 2.31.8-nompi, 2.31.8-openmpi-1.6.5, 2.31.8-openmpi-1.8.1, 2.31.8-openmpi-1.8.8, 2.31.9-openmpi-1.8.1

    Genome annotation pipeline
    http://www.yandell-lab.org/software/maker.html
    Info: http://www.yandell-lab.org/software/maker_docs.html
    Info: /group/bioinfo/apps/apps/MAKER-2.31.9-nompi/README
    Tutorial: http://gmod.org/wiki/MAKER_Tutorial
    Forum: http://groups.google.com/group/maker-devel

    This version does not support MPI.

    Depends on SNAP
    Depends on RepeatMasker
    Depends on exonerate
    Depends on blast
    Depends on AUGUSTUS
    Depends on GeneMark

  537. MapSplice
  538. module name: MapSplice
    version 2.2.1

    Mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome
    http://www.netlab.uky.edu/p/bioinfo/MapSplice2
    Manual: http://www.netlab.uky.edu/p/bioinfo/MapSplice2UserGuide

    Depends on gcc

  539. MAQ
  540. module name: maq
    version 0.7.1

    MAQ: Mapping and Assembly with Qualities
    http://maq.sourceforge.net/
    http://sourceforge.net/projects/maq/files/maq
    Manual: http://maq.sourceforge.net/maq-man.shtml
    FAQ: http://maq.sourceforge.net/faq.shtml

    Depends on gcc

  541. MaSuRCA (Maryland Super Read Celera Assembler)
  542. module name: MaSuRCA
    version 3.2.3
    Other versions: 2.1.0, 3.1.3, 3.2.2, 3.2.2_RC1

    Genome assembler
    http://www.genome.umd.edu/masurca.html
    Info: man jellyfish

    Create sample config file with: masurca -g config.txt
    Put in assembly directory and modify as needed

    Depends on gcc
    Depends on Boost

  543. MATLAB Compiler Runtime (MCR)
  544. module name: MCR
    version 7.14

    Shared libraries that enables the execution of compiled MATLAB applications
    http://www.mathworks.com/products/compiler/mcr/
    Corresponds to MATLAB R2010b

  545. matrix2png
  546. module name: matrix2png
    version 1.2.2

    Visualizations of microarray data and many other data types
    http://www.chibi.ubc.ca/matrix2png/
    Manual at http://www.chibi.ubc.ca/matrix2png/matrix2image.html
    Examples at http://www.chibi.ubc.ca/matrix2png/matrix2png-samples.html

    Depends on gcc

  547. Mauve
  548. module name: mauve
    version 2015-02-13
    Other versions: 2.3.1

    http://darlinglab.org/mauve/mauve.html
    Construct multiple genome alignments in the presence of
    large-scale evolutionary events such as rearrangement and inversion
    Manual: http://darlinglab.org/mauve/user-guide/introduction.html
    Note: Needs X11 support for GUI (not needed with command line
    utilities mauveAligner or progressiveMauve)


    Depends on java

  549. MaxBin
  550. module name: MaxBin
    version 2.2.3

    Binning assembled metagenomic sequences based on an Expectation-Maximization algorithm
    https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
    FAQ: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html#faq

    Depends on gcc
    Depends on bowtie2/2.2.3
    Depends on HMMER/3.1b2
    Depends on idba/1.1.1
    Depends on FragGeneScan/1.30
    Depends on R-bioconductor/3.3.3

  551. mbuffer
  552. module name: mbuffer
    version 20150412

    Tool for buffering data streams
    http://www.maier-komor.de/mbuffer.html
    Info: /group/bioinfo/apps/apps/mbuffer-20150412/README
    Info: man mbuffer

    Depends on gcc

  553. mcl
  554. module name: mcl
    version 14-137
    Other versions: 12-068

    The Markov Cluster Algorithm (MCL)
    MCL algorithm finds cluster structure in graphs
    http://www.micans.org/mcl/index.html
    man pages available

    Depends on gcc

  555. MCScanX
  556. module name: MCScanX
    version 2366066597

    Multiple Collinearity Scan toolkit
    http://chibba.pgml.uga.edu/mcscan2/
    Manual: http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf

    Depends on gcc
    Depends on java
    Depends on perl

  557. mdust
  558. module name: mdust
    version 2006-10-17

    Mask Low-Complexity DNA Sequences
    https://github.com/lh3/mdust
    ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/

  559. MeDUSA
  560. module name: medusa
    version 1.0

    Pipeline for MeDIP-seq data analysis
    http://www2.cancer.ucl.ac.uk/medicalgenomics/medusa/
    Info at /group/bioinfo/apps/apps/medusa-1.0/README
    Copy and change the config file in
    /group/bioinfo/apps/apps/medusa-1.0/config_files/medusa_template.cfg

    Depends on perl
    Depends on R-bioconductor
    Depends on bwa
    Depends on samtools
    Depends on fastqc
    Depends on USeq
    Depends on BEDTools

  561. Medusa
  562. module name: VarScan
    version 2.3.9

    http://dkoboldt.github.io/varscan/
    Variant detection in massively parallel sequencing data
    Info at /group/bioinfo/apps/apps/VarScan-2.3.9/help.txt
    Run using:
    java -jar $VARSCAN_JAR

    Includes fpfilter.pl and mergeSegments.pl


    Depends on java

  563. MeFiT (Merging and Filtering Tool for Paired-End Reads)
  564. module name: MeFiT
    version 1.0

    Pipeline to merge overlapping paired-end reads, calculate merge statistics, and filter reads for quality
    https://github.com/nisheth/MeFiT
    Example data in /group/bioinfo/apps/apps/MeFiT-1.0/sample
    Probably need to copy /group/bioinfo/apps/apps/MeFiT-1.0/casper.params

    Depends on biopython/2.7.11
    Depends on CASPER

  565. MEGAN (MEtaGenome ANalyzer) Community Edition
  566. module name: MEGAN
    version 6.8.0
    Other versions: 4.70.4, 5.1.4, 5.2.3, 6.4.8, 6.5.7

    Software for analyzing metagenomes
    http://ab.inf.uni-tuebingen.de/software/megan5/
    Manual: /group/bioinfo/apps/apps/MEGAN-6.8.0/manual.pdf
    Manual: http://ab.inf.uni-tuebingen.de/data/software/megan6/download/manual.pdf
    Release Notes: http://ab.inf.uni-tuebingen.de/data/software/megan6/download/release_notes.txt
    Need X11 support for program to run (ssh -X)
    Configured to use 8 GB of memory

    Depends on java/8

  567. MEME suite (Multiple Em for Motif Elicitation)
  568. module name: meme
    version 4.10.1

    Discovers novel, ungapped motifs in nucleotide or protein sequences
    http://meme-suite.org/index.html
    This includes the command-line programs but not the web server

    Public web server: http://meme-suite.org/tools/meme
    Info in /group/bioinfo/apps/apps/meme-4.10.1/doc
    Release notes: http://meme-suite.org/doc/release-notes.html
    Manual: http://meme-suite.org/doc/overview.html
    FAQ: http://meme-suite.org/doc/general-faq.html
    Forum: https://groups.google.com/forum/#!forum/meme-suite

    Depends on openmpi/1.8.1_gcc-4.7.2
    Depends on perl/5.20.1
    Depends on biopython/2.7.8

  569. MeQA
  570. module name: MeQA
    version 1.0.0

    A pipeline for MeDIP-seq data quality assessment and analysis
    http://life.tongji.edu.cn/meqa/
    Need to copy /group/bioinfo/apps/apps/MeQA-1.0.0/example-config.cfg
    to your project dir and modify to suit your needs

    Depends on R-bioconductor
    Depends on biopython/2.7.2
    Depends on bwa
    Depends on samtools
    Depends on BEDTools
    Depends on samstat
    Depends on CEAS

  571. MetaCV
  572. module name: metacv
    version 2.2.9

    Composition based classification for short metagenomic sequences
    http://metacv.sourceforge.net/
    Manual: /group/bioinfo/apps/apps/metacv-2.2.9/MetaCV_manual.pdf
    Need to install prokaryotes database from website (>16GB compressed)

    Depends on gcc

  573. MetaPhlAn: Metagenomic Phylogenetic Analysis
  574. module name: metaphlan2
    version 2.6.0

    Profiling the composition of microbial communities from metagenomic shotgun sequencing data.
    http://huttenhower.sph.harvard.edu/metaphlan2

    Precomputed BLAST and bowtie2 mpa databases at
    - /group/bioinfo/apps/apps/metaphlan-2.6.0/db_v20

    Forum: https://groups.google.com/forum/#!forum/metaphlan-users
    FAQ: https://bitbucket.org/nsegata/metaphlan/wiki/FAQ
    Tutorial: http://bitbucket.org/biobakery/biobakery/wiki/metaphlan2

    Depends on biopython/2.7.12
    Depends on blast
    Depends on bowtie2

  575. MetaTrans
  576. module name: MetaTrans
    version 1.0

    Metatranscriptomic sequence analysis pipeline
    http://www.metatrans.org/
    Manual: /group/bioinfo/apps/apps/MetaTrans-1.0/manual.pdf

    You need to make a copy of the program and data into a directory owned
    by you before you can use it.

    Depends on R-bioconductor/3.3.0
    Depends on biopython/2.7.11
    Depends on usearch

  577. MetaVelvet
  578. module name: MetaVelvet
    version 1.2.01

    A short read assember for metagenomics
    http://metavelvet.dna.bio.keio.ac.jp/
    Built with MAX KMER LENGTH=99 and CATEGORIES=4

    Depends on velvet

  579. methylQA
  580. module name: methylQA
    version 0.1.5

    Methylation sequencing data quality assessment tool
    http://methylqa.sourceforge.net/index.php
    Tutorial: http://methylqa.sourceforge.net/tutorial.php

    Depends on gcc
    Depends on R-bioconductor/3.1.2
    Depends on texlive

  581. metilene
  582. module name: metilene
    version 0.2-4

    Fast and sensitive detection of differential DNA methylation
    https://www.bioinf.uni-leipzig.de/Software/metilene/
    Manual: /group/bioinfo/apps/apps/metilene_v0.2-4/manual.pdf

    Depends on gcc

  583. METIS
  584. module name: metis
    version 5.0.2

    Serial Graph Partitioning and Fill-reducing Matrix Ordering
    http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
    Manual: http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/manual.pdf
    Manual: /group/bioinfo/apps/apps/metis-5.0.2/manual/manual.pdf

    Depends on gcc

  585. MFEprimer
  586. module name: MFEprimer
    version 2.0-246f757

    A fast thermodynamics-based program for checking PCR primer specificity
    https://github.com/quwubin/MFEprimer
    Manual: https://github.com/quwubin/MFEprimer/wiki/Manual
    On-line: http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0/
    Info: /group/bioinfo/apps/apps/MFEprimer-2.0-246f757/README.md

    Probably need to install in home directory if you want to use your own custom database

    Depends on biopython/2.7.8

  587. Microbiome Utilities Portal of the Broad Institute
  588. module name: microbiomeutil
    version r20110519

    Provides microbiome utilities :
    - Sequence alignment (NAST-iEr)
    - Chimera detection (ChimeraSlayer, WigeoN)
    - Operational taxonomic unit OTU binning (TreeChopper)
    - Sequence assembly (AmosCmp16Spipeline)
    - database of reference 16S sequences
    http://microbiomeutil.sourceforge.net/
    Info: /group/bioinfo/apps/apps/microbiomeutil-r20110519/docs

    Depends on blast/2.2.26
    Depends on cdbtools

  589. MicroRazerS
  590. module name: MicroRazerS
    version 1.0

    Fast mapping short RNAs onto a reference genome
    http://www.seqan.de/projects/MicroRazerS/
    Mailing list: https://lists.fu-berlin.de/pipermail/seqan-dev/

    Depends on gcc

  591. MinCED (Mining CRISPRs in Environmental Datasets)
  592. module name: minced
    version 0.2.0

    Find CRISPRs in genomes or metagenomes
    https://github.com/ctSkennerton/minced/

    Depends on java

  593. Minia
  594. module name: minia
    version 1.5418
    Other versions: 1.5418-maxk128, maxk128, maxk32

    Short-read assembler based on a de Bruijn graph
    http://minia.genouest.org/
    Manual: /group/bioinfo/apps/apps/minia-1.5418/manual.pdf
    This version is compiled with support for maximum k-mer size of 32

    Depends on gcc

  595. Miniconda
  596. module name: conda
    version 4.3.21
    Other versions: 4.3.11

    Package, dependency and environment management for any language
    https://github.com/conda/conda
    https://conda.io/docs/index.html


  597. MinPath (Minimal set of Pathways)
  598. module name: MinPath
    version 1.2

    Biological pathway reconstructions using protein family predictions
    http://omics.informatics.indiana.edu/MinPath/


    Depends on biopython/2.7.12

  599. MIRA
  600. module name: mira
    version 4.0.2
    Other versions: 3.4.1.1, 3.9.1, 3.9.10, 3.9.11, 3.9.12, 3.9.14, 3.9.15, 3.9.16, 3.9.18, 3.9.3, 3.9.4, 3.9.5, 3.9.7, 3.9.8, 3.9.9, 4.0, 4.0.1, 4.0rc1, 4.0rc2, 4.0rc3, 4.0rc4, 4.0rc5, 4.9.1, 4.9.3, 4.9.4, 4.9.5

    Whole genome shotgun and EST sequence assembler
    http://sourceforge.net/p/mira-assembler/wiki/Home/
    Manual at http://mira-assembler.sourceforge.net/docs-dev/DefinitiveGuideToMIRA.html
    Docs at /group/bioinfo/apps/apps/mira-4.0.2/docs
    Mailing lists: http://www.chevreux.org/mira_mailinglists.html

    Depends on gcc
    Depends on tcl

  601. miRanda
  602. module name: miRanda
    version 3.3a

    microRNA Target Detection Software
    http://www.microrna.org/microrna/getDownloads.do
    Manual: man miranda
    Manual: http://cbio.mskcc.org/microrna_data/manual.html

    Depends on gcc

  603. miRDeep
  604. module name: mirdeep
    version 2.0.0.8
    Other versions: 2.0.0.4, 2.0.0.7

    Discovering known and novel miRNAs from deep sequencing data
    http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/index.html
    Manual at http://www.mdc-berlin.de/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/documentation.html
    Tutorial: /group/bioinfo/apps/apps/mirdeep-2.0.0.8/TUTORIAL

    Depends on perl
    Depends on bowtie
    Depends on ViennaRNA
    Depends on randfold
    Depends on squid

  605. miRDeep*
  606. module name: miRDeep-star
    version 37

    miRNA identification from RNA sequencing data
    http://www.australianprostatecentre.org/research/software/mirdeep-star
    Manual: /group/bioinfo/apps/apps/miRDeep_star_v37/manual.pdf

    Configured to use 8GB of memory
    Need X11 support for program to run (ssh -X)

    You need to make a copy of the program and data into a directory owned
    by you before you can use it. The steps below will copy everything
    into a directory in your home directory:

    $ cd $HOME
    $ cp -r $MDS_HOME $HOME # 6 GB of data will be copied

    Now you have your own copy of the program and data. You only need to
    do the above steps one time. Every time you want to run the program,
    do the following steps:

    $ cd miRDeep_star_v37
    $ ./miRDeep_star.sh # starts the program


    Depends on java/8

  607. miRDeep-P
  608. module name: miRDeep-P
    version 1.3

    A computational tool for analyzing the microRNA transcriptome in plants
    http://faculty.virginia.edu/lilab/miRDP/
    Manual at http://faculty.virginia.edu/lilab/miRDP/miR_material/miRDP_manual1.3.pdf
    Manual at /group/bioinfo/apps/apps/miRDP-1.3/miRDP_manual1.3.pdf

    Depends on perl
    Depends on bowtie
    Depends on ViennaRNA
    Depends on randfold

  609. MIREAP
  610. module name: mireap
    version 0.2

    Reap miRNAs from deeply sequenced smRNA library
    http://sourceforge.net/projects/mireap/

    Depends on ViennaRNA
    Depends on perl/5.16.1

  611. miRExpress
  612. module name: miRExpress
    version 2.1.4
    Other versions: 2.1.3

    Analyzing high-throughput sequencing data for profiling microRNA expression
    http://mirexpress.mbc.nctu.edu.tw/
    Usage: /group/bioinfo/apps/apps/miRExpress-2.1.4/README
    Data avail for download from http://mirexpress.mbc.nctu.edu.tw/

    Depends on gcc

  613. miRNAkey
  614. module name: miRNAkey
    version 1.2

    A pipeline microRNA Deep Sequencing data analysis
    http://ibis.tau.ac.il/miRNAkey/
    Manual: http://ibis.tau.ac.il/miRNAkey/man.html
    Need to copy /group/bioinfo/apps/apps/miRNAkey-1.2
    to your project directory and run from there

    Depends on java
    Depends on bwa
    Depends on fastx
    Depends on perl

  615. miRquant
  616. module name: miRquant
    version 2.0

    Detect miRNAs in smRNA-seq data
    https://github.com/Sethupathy-Lab/miRquant
    Tutorial: https://github.com/Sethupathy-Lab/miRquant/blob/master/tutorial/TUTORIAL.md

    Need to make copy of miRquant files to your own directory and run from there.
    For example:
    cd $RCAC_SCRATCH
    cp -rp $MIRQUANT_HOME ./.
    cd miRquant-2.0
    # download genomes, modify files in "configuration" directory, etc


    Depends on cutadapt/1.12
    Depends on BEDTools/2.25.0
    Depends on bowtie/1.1.0
    Depends on SHRiMP/2.2.2
    Depends on R-bioconductor/3.3.0

  617. MITE-Hunter
  618. module name: MITE-Hunter
    version 11-2011

    Find miniature inverted-repeat transposable elements from genomic sequences
    http://target.iplantcollaborative.org/mite_hunter.html
    https://www.ncbi.nlm.nih.gov/pubmed/20880995
    https://github.com/jburnette/MITE-Hunter
    Manual: http://target.iplantcollaborative.org/mite_hunter/MITE-Hunter_manual.pdf
    Manual: /group/bioinfo/apps/apps/MITE-Hunter-11-2011/manual.docx

    Depends on blast/2.2.26
    Depends on mdust
    Depends on muscle

  619. MITObim
  620. module name: MITObim
    version 1.8
    Other versions: 1.6, 1.7

    Mitochondrial baiting and iterative mapping
    https://github.com/chrishah/MITObim
    Info: /group/bioinfo/apps/apps/MITObim-1.8/README.md
    Test data: /group/bioinfo/apps/apps/MITObim-1.8/testdata1.tgz

    Depends on perl
    Depends on mira/4.0.2

  621. MOCAT (Metagenomics Analysis Toolkit)
  622. module name: MOCAT
    version 2.0.0

    Pipeline for processing Illumina metagenomic data
    http://mocat.embl.de/index.html
    Tutorial: http://mocat.embl.de/tutorial.html


    Depends on perl
    Depends on GeneMark
    Depends on usearch/8

  623. mod-primer3
  624. module name: mod-primer3
    version 2.2.3

    Modified primer3 software used by edittag
    https://github.com/faircloth-lab/mod-primer3
    Thermodynamic parameter files located in:
    /group/bioinfo/apps/apps/mod-primer3-2.2.3/src/primer3_config/

    Depends on gcc

  625. Mono
  626. module name: mono
    version 4.0.2

    Cross platform, open source .NET framework
    http://www.mono-project.com/

    Depends on gcc

  627. MOTHUR
  628. module name: mothur
    version 1.39.3
    Other versions: 1.25.0, 1.25.1, 1.32.1, 1.34.4, 1.37.2, 1.37.6

    Microbial ecology tools
    mothur and uchime (not GUI version)
    http://www.mothur.org/
    wiki: http://www.mothur.org/wiki
    forum: http://www.mothur.org/forum

    Depends on gcc

  629. MrBayes
  630. module name: mrbayes
    version 3.2.6
    Other versions: 3.2.1, 3.2.5

    Bayesian Inference of Phylogeny
    http://mrbayes.sourceforge.net/download.php
    Manual at http://mrbayes.sourceforge.net/manual.php

    Depends on beagle/2.1.2
    Depends on gcc
    Depends on openmpi

  631. MSPC (Multiple Sample Peak Calling)
  632. module name: MSPC
    version 1.1.0.0
    Other versions: 1.0.0.0

    Using combined evidence from replicates to evaluate ChIP-seq peaks
    http://www.bioinformatics.deib.polimi.it/genomic_computing/MSPC/index.html
    Info: http://www.bioinformatics.deib.polimi.it/genomic_computing/MSPC/documentation.html

    Wrapper script provided; use "MSPC" command

    Depends on mono

  633. Mugsy
  634. module name: Mugsy
    version 1r2.3

    Multiple whole genome alignment tool
    http://mugsy.sourceforge.net/

    Depends on gcc
    Depends on muscle

  635. MultiQC
  636. module name: MultiQC
    version 0.8

    Aggregate results from bioinformatics analyses across many samples into a single report
    http://multiqc.info/

    Depends on biopython/2.7.11

  637. MUMmer
  638. module name: MUMmer
    version 3.23

    Ultra-fast alignment of large-scale DNA and protein sequences
    http://mummer.sourceforge.net/
    Manual: http://mummer.sourceforge.net/manual
    Tutorial: http://mummer.sourceforge.net/examples
    Info: /group/bioinfo/apps/apps/MUMmer-3.23/docs

    Depends on gcc

  639. MUSCLE
  640. module name: muscle
    version 3.8.31
    Other versions: 3.8.425

    Multiple sequence alignment (faster than clustalw)
    http://www.drive5.com/muscle/
    Docs: http://www.drive5.com/muscle/docs.htm

  641. MuSE
  642. module name: MuSE
    version 1.0-rc

    Somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data.
    http://bioinformatics.mdanderson.org/main/MuSE


    Depends on gcc

  643. MySQL Connector/J
  644. module name: mysql-connector-java
    version 5.1.21
    Other versions: 5.0.5, 5.0.8

    MySQL Connector/J is the official JDBC driver for MySQL
    http://www.mysql.com/products/connector/
    Docs: /group/bioinfo/apps/apps/mysql-connector-java-5.1.21/docs

    Depends on java

  645. NCBI BLAST
  646. module name: blast
    version 2.6.0+
    Other versions: 2.2.22, 2.2.25+, 2.2.26, 2.2.26+, 2.2.27+, 2.2.28+, 2.2.29+, 2.2.30+, 2.2.31+, 2.3.0+, 2.4.0+, 2.5.0+, 2.7.1+

    Basic Local Alignment Search Tool
    http://blast.ncbi.nlm.nih.gov/
    News: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
    Manuals: http://www.ncbi.nlm.nih.gov/books/NBK1762
    User Manual: http://www.ncbi.nlm.nih.gov/books/NBK279690
    Release notes: http://www.ncbi.nlm.nih.gov/books/NBK131777
    Versioning info: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=VersioningBlast

    Includes RMBlast (for use with RepeatMasker)

    Depends on gcc

  647. NCBI BLAST CGI programs
  648. module name: wwwblast
    version 2.2.26

    BLAST CGI programs (legacy version)
    http://blast.ncbi.nlm.nih.gov/
    Docs: /group/bioinfo/apps/apps/wwwblast-2.2.26/docs

    This "legacy" version of NCBI BLAST is deprecated; see
    http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
    for reasons to use BLAST+ instead

    These are the wwwblast CGI programs. They are designed to be run by a
    web server.

    Depends on gcc

  649. NCBI Entrez Direct
  650. module name: edirect
    version 1.40

    Entrez utilities on the UNIX command line
    http://www.ncbi.nlm.nih.gov/news/02-06-2014-entrez-direct-released/
    Docs: http://www.ncbi.nlm.nih.gov/books/NBK179288/
    Docs: /group/bioinfo/apps/apps/edirect-1.40/README

  651. NCBI Magic-BLAST
  652. module name: magic-blast
    version 1.3.0
    Other versions: 1.1.0, 1.2.0

    Map next-gen RNA/DNA sequencing runs against a whole genome or transcriptome
    https://ncbi.github.io/magicblast/
    https://ncbiinsights.ncbi.nlm.nih.gov/tag/magic-blast/
    Info: /group/bioinfo/apps/apps/ncbi-magicblast-1.3.0/README

    Depends on gcc

  653. NCBI nseg
  654. module name: nseg
    version 1995-09-28

    Might have something to do with repeat library filtering?
    ftp://ftp.ncbi.nih.gov/pub/seg/nseg/
    No official instructions or documention?
    Mentioned in RepeatScount README:
    http://bix.ucsd.edu/repeatscout/readme.1.0.5.txt

    Depends on gcc

  655. NcFTP client
  656. module name: ncftp
    version 3.2.6

    FTP client
    http://www.ncftp.com/

    Depends on gcc

  657. ncoils
  658. module name: ncoils
    version 2.2

    Secondary structure predictions from protein sequences
    The algorithm was published in Lupas, van Dyke & Stock, Predicting coiled coils from protein sequences Science, 252, 1162-1164, 1991

    Depends on gcc

  659. NetBeans IDE
  660. module name: netbeans
    version 7.4

    Develop applications with Java
    https://netbeans.org/
    https://netbeans.org/community/releases/74/
    Info: https://netbeans.org/kb/index.html
    Needs X11 support

    Depends on java

  661. NetBox
  662. module name: netbox
    version 22-May-2014

    Perform network analysis on human interaction networks
    http://cbio.mskcc.org/tools/netbox/
    Docs: http://cbio.mskcc.org/wp-content/uploads/2012/10/netbox_readme.pdf
    Docs: /group/bioinfo/apps/apps/netbox-22-May-2014/netbox_readme.pdf

    Must make private copy of database files before using:
    $ module load netbox
    $ mkdir netbox_db
    $ cd netbox_db
    $ cp -r $NETBOX_HOME/db ./.
    $ cp -r $NETBOX_HOME/config ./.
    $ export NETBOX_HOME=`pwd`

    If using csh or tcsh, change last line to:
    % setenv NETBOX_HOME `pwd`

    Depends on java
    Depends on biopython/2.7.3

  663. NetCDF (Network Common Data Format)
  664. module name: NetCDF
    version 4.4.1.1

    https://www.unidata.ucar.edu/software/netcdf/
    Software libraries and data formats for the creation, access, and sharing of array-oriented scientific data.

    Depends on gcc
    Depends on curl/7.46.0
    Depends on zlib/1.2.11
    Depends on HDF5/1.8.19

  665. Netpbm
  666. module name: netpbm-progs
    version 10.35.58-10.e15.x86_64

    Toolkit for manipulation of graphic images
    http://netpbm.sourceforge.net/
    http://pkgs.org/centos-5-rhel-5/centos-rhel-x86_64/netpbm-progs-10.35.58-10.el5.x86_64.rpm/download/
    Manual pages available

  667. NextClip
  668. module name: nextclip
    version 0.7

    Quality analysis and read preparation for Nextera long mate pair (LMP) libraries
    http://www.tgac.ac.uk/nextclip/
    Manual: /group/bioinfo/apps/apps/nextclip-0.7/nextclipmanual.pdf
    Needs TeX Live 2012 or newer software to generate PDF report.

    Depends on gcc
    Depends on bwa
    Depends on R-bioconductor
    Depends on texlive

  669. ngs-bits
  670. module name: ngs-bits
    version May-27-2016

    Short-read seqencing tools
    https://github.com/imgag/ngs-bits
    Includes SeqPurge

    Depends on biopython/2.7.8

  671. ngsplot
  672. module name: ngsplot
    version 2.61
    Other versions: 2.41.3, 2.47, 2.63

    Visualize next-generation sequencing (NGS) samples at functional genomic regions
    https://code.google.com/p/ngsplot/
    Example data: /group/bioinfo/apps/apps/ngsplot-2.61/example

    Depends on R-bioconductor/3.1.0
    Depends on biopython/2.7.8

  673. NGSUtils
  674. module name: ngsutils
    version 0.5.9

    Tools for next-generation sequencing analysis
    http://ngsutils.org/
    https://github.com/ngsutils/ngsutils

    This probably does not work

    Depends on biopython/2.7.12
    Depends on samtools
    Depends on tabix

  675. Novocraft
  676. module name: novocraft
    version 3.02.12
    Other versions: 2.07.05, 2.07.13, 2.08.01, 2.08.02

    Next-Generation Sequencing analysis suite
    http://www.novocraft.com/products/novoalign/
    Manual: http://www.novocraft.com/documentation/novoalign-2/
    Manual: some PDF files in /group/bioinfo/apps/apps/novocraft-3.02.12

  677. NPS (Nucleosome Positioning from Sequencing)
  678. module name: NPS
    version 1.3.2

    Identify nucleosome positions given histone-modification ChIP-seq or
    nucleosome sequencing at the nucleosome level.
    http://liulab.dfci.harvard.edu/NPS/

    Might need to copy program files to home directory and run there:
    mkdir ~/NPS
    cd ~/NPS
    cp $NPS_HOME/* ~/NPS

    Depends on biopython/2.7.3

  679. NSeq
  680. module name: NSeq
    version 1.0

    Nucleosome positioning
    https://github.com/songlab/NSeq

    Depends on java

  681. numexpr
  682. module name: numexpr
    version 2.6.2
    Other versions: 1.7.3

    Fast numerical array expression evaluator for Python, NumPy, PyTables, pandas, bcolz and more
    https://github.com/pydata/numexpr

    Depends on biopython/2.7.12

  683. Oases
  684. module name: oases
    version 0.2.08
    Other versions: 0.02.05, 0.02.06, 0.02.08

    De novo transcriptome assembler for very short reads
    http://www.ebi.ac.uk/~zerbino/oases/
    Manual at /group/bioinfo/apps/apps/oases_0.2.08/doc/OasesManual.pdf
    Includes colorspace version oases_de as well as oases

    Build parameters:
    - MAXKMERLENGTH=99
    - CATEGORIES=4
    - OPENMP=1

    Depends on gcc
    Depends on biopython/2.7.3
    Depends on velvet

  685. OpenMPI
  686. module name: OpenMPI
    version 1.8.8_gcc-4.7.2
    Other versions: 1.6.5_gcc-4.7.2

    A High Performance Message Passing Library
    http://www.open-mpi.org/

    Depends on gcc/4.7.2

  687. OrthoFiller
  688. module name: OrthoFiller
    version 1.1.4

    Identify missing annotations for evolutionarily conserved genes
    https://github.com/mpdunne/orthofiller

    Depends on OrthoFinder
    Depends on BEDTools/2.25.0
    Depends on R-bioconductor/3.4.0
    Depends on AUGUSTUS
    Depends on HMMER
    Depends on gff3togtf

  689. OrthoFilter
  690. module name: OrthoFinder
    version 2.1.2
    Other versions: 1.1.8

    Accurate inference of orthologous gene groups made easy
    https://github.com/davidemms/OrthoFinder
    Manual: /group/bioinfo/apps/apps/OrthoFinder-2.1.2/OrthoFinder-manual.pdf
    Manual: /group/bioinfo/apps/apps/OrthoFinder-2.1.2/OrthoFinder-options.pdf
    Example data: /group/bioinfo/apps/apps/OrthoFinder-2.1.2/ExampleData

    Depends on blast
    Depends on mcl
    Depends on FastME
    Depends on mafft
    Depends on FastTree

  691. OrthoMCL DB
  692. module name: orthomcl
    Ortholog Groups of Protein Sequences from Multiple Genomes
    version 2.0.9
    Other versions: 2.0.3, 2.0.8

    http://orthomcl.org/orthomcl/
    Info: /group/bioinfo/apps/apps/orthomcl-2.0.9/doc/OrthoMCLEngine/Main/UserGuide.txt
    Need to use relational database (like MySQL)

    Depends on perl
    Depends on mcl
    Depends on blast

  693. OrthoMCL: Ortholog Clustering Analysis
  694. module name: omcl
    version 1.4

    http://arthropods.eugenes.org/EvidentialGene/evigene/scripts/omcl/
    Info: /group/bioinfo/apps/apps/omcl-1.4/orthomcl_readme.txt

    Copy software to your own directory and run from there:
    cp -rp $OMCL_ROOT $RCAC_SCRATCH
    export PATH=$RCAC_SCRATCH/omcl-1.4:$PATH

    Read /group/bioinfo/apps/apps/omcl-1.4/orthomcl_readme.txt
    then edit $RCAC_SCRATCH/omcl-1.4/orthomcl_modevg.pm

    This software is not tested and probably does not work.

    Depends on perl
    Depends on mcl/12-068
    Depends on blast/2.2.26

  695. PAGIT
  696. module name: PAGIT
    version 1.0

    Post Assembly Genome Improvement Toolkit
    Generate sequence by ordering contigs, closing gaps, correcting errors and transferring annotation.
    http://www.sanger.ac.uk/resources/software/pagit/
    Note: This program doesn't work

    Depends on gcc
    Depends on java

  697. PALS (Pairwise Aligner for Long Sequences)
  698. module name: PALS
    version 1.0

    Finds local alignments between DNA sequences
    http://drive5.com/pals/
    User's Guide: /group/bioinfo/apps/apps/PALS-1.0/manual.pdf
    Warning: PALS is obsolete and no longer supported

    Depends on gcc

  699. PAML (Phylogenetic Analysis by Maximum Likelihood)
  700. module name: PAML
    version 4.8

    Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
    http://abacus.gene.ucl.ac.uk/software/paml.html
    Manuals in /group/bioinfo/apps/apps/PAML-4.8/doc/
    Examples in /group/bioinfo/apps/apps/PAML-4.8/examples/

    You may need to copy data and control files into your working directory:
    $ cp $paml_data/* paml/work/dir
    $ cd paml/work/dir
    $ baseml ...

    Depends on gcc

  701. PANDAseq
  702. module name: pandaseq
    version 2.8.1
    Other versions: 0.6t, 2.0, 2.3, 2.3-RDP-1.0.3, 2.5, 2.6

    PAired-eND Assembler for DNA sequences
    https://github.com/neufeld/pandaseq
    Paper: http://www.biomedcentral.com/1471-2105/13/31/
    Wiki at https://github.com/neufeld/pandaseq/wiki
    man pages for pandaseq, pandaxs, pandaseq-checkid, pandaseq-diff and pandaseq-hang

    Depends on gcc

  703. Parallel-meta
  704. module name: parallel-meta
    version 2.4

    Metagenomic analysis pipeline
    https://github.com/Comp-Bio-Group/Parallel-META
    Manual: /group/bioinfo/apps/apps/parallel-meta-2.4/manual/Parallel-meta-2.4.pdf
    Need to run with X11 support to generate plots:
    https://www.rcac.purdue.edu/compute/conte/guide/#accounts_login_x11

    Depends on gcc
    Depends on R-bioconductor/3.1.0
    Depends on HMMER
    Depends on blast/2.2.26
    Depends on velvet/1.2.10
    Depends on FragGeneScan/1.19

  705. ParsInsert
  706. module name: ParsInsert
    version 1.04

    Produces both a phylogenetic tree and taxonomic classification for
    sequences for microbial community sequence analysis
    http://parsinsert.sourceforge.net/
    Info: /group/bioinfo/apps/apps/ParsInsert-1.04/ReleaseNotes.txt


    Depends on gcc

  707. PartitionFinder
  708. module name: partitionfinder
    version 2.1.1

    Discovers optimal partitioning schemes for DNA sequences
    http://www.robertlanfear.com/partitionfinder/

    Depends on biopython/2.7.12

  709. PASA_Lite (PASA without MySQL dependency)
  710. module name: PASA_Lite
    version 0.1.0

    Eukaryotic genome annotation tool
    https://github.com/PASApipeline/PASA_Lite

    Depends on perl
    Depends on gmap
    Depends on fasta/35
    Depends on seqclean
    Depends on blat

  711. PASHA: Parallelized Short Read Assembly
  712. module name: PASHA
    version 1.0.10

    Parallel short read assemblers for large genomes
    https://sourceforge.net/projects/pasha/
    http://pasha.sourceforge.net/homepage.htm

    Depends on gcc
    Depends on openmpi
    Depends on tbb

  713. patchelf
  714. module name: patchelf
    http://nixos.org/patchelf.html
    Modify the dynamic linker and RPATH of ELF executables

    Depends on gcc

  715. PBSuite
  716. module name: PBSuite
    version 15.8.24
    Other versions: 14.9.9

    http://sourceforge.net/projects/pb-jelly/
    Software for Long-Read Sequencing Data from PacBio
    Info: /group/bioinfo/apps/apps/PBSuite_15.8.24/docs

    Depends on blasr
    Depends on biopython/2.7.8

  717. PCAP (Parallel Contig Assembly Program)
  718. module name: PCAP
    version 06-07-05

    Assembles large genomes
    http://seq.cs.iastate.edu/
    https://banana-slug.soe.ucsc.edu/bioinformatic_tools:cap3_pcap
    Manual: See directory /group/bioinfo/apps/apps/PCAP-06-07-05
    read files: README, Doc, Doc.rep, Distributed.doc

    To use autopcap, read the file autopcap.doc
    You probably need to copy all the files in /group/bioinfo/apps/apps/PCAP-06-07-05
    into your home directory and put your data into a subdirectory
    (like was done in the "example" subdirectory.)

    Depends on gcc

  719. PCRE
  720. module name: pcre
    version 8.38

    Perl Compatible Regular Expressions
    http://www.pcre.org/
    man pages available
    Info: /group/bioinfo/apps/apps/pcre-8.38/share/doc

    Build options were:
    --enable-utf
    --enable-unicode-properties
    --enable-jit --disable-cpp
    --enable-pcretest-libreadline
    --enable-pcregrep-libz
    --enable-pcregrep-libbz2

    Depends on gcc
    Depends on zlib
    Depends on bzip2

  721. PeakSplitter
  722. module name: PeakSplitter
    version 1.0

    Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks
    http://www.ebi.ac.uk/bertone/software.html
    Usage: /group/bioinfo/apps/apps/PeakSplitter-1.0/README

    Depends on java

  723. PEAR - Paired-End reAd mergeR
  724. module name: pear
    version 0.9.6
    Other versions: 0.9.10

    Pair-end read merger
    http://sco.h-its.org/exelixis/web/software/pear/

  725. PEP scaffolder
  726. module name: PEP-scaffolder
    version Mar-28-2016

    Scaffolding tool using (homologous) proteins to scaffold genome fragments
    http://www.fishbrowser.org/software/PEP_scaffolder/index.php?action=isin

  727. Perl
  728. module name: perl
    version 5.20.1
    Other versions: 5.16.0, 5.16.1, 5.18.1

    Programming language
    http://www.perl.org/
    Manual: http://www.perl.org/docs.html
    Includes support for perl threads
    Built as shared perl library
    Bioperl 1.6.924
    Bio-SamTools-1.39 using samtools 0.1.19 library
    Bio-BigFile-1.07 using Sep 2 2014 Jim Kent library

    Depends on gcc
    Depends on gnuplot
    Depends on tidyp
    Depends on gsl/2.3
    Depends on ImageMagick/6.8.9-8
    Depends on expat

  729. Phobius
  730. module name: phobius
    version 1.01

    A combined transmembrane topology and signal peptide predictor
    http://phobius.sbc.su.se/

    Depends on gcc

  731. Phobos
  732. module name: phobos
    version 3.3.12

    Tandem repeat search tool for complete genomes
    http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm
    Manual: /group/bioinfo/apps/apps/phobos-v3.3.12-linux/phobos-manual-3.3.12.pdf
    Info: /group/bioinfo/apps/apps/phobos-v3.3.12-linux/Quickstart.txt

    Depends on gcc

  733. phrap
  734. module name: phrap
    version 1.080812
    Other versions: 1.090518

    Assemble shotgun DNA sequence data
    http://www.phrap.org/phredphrapconsed.html
    Manual: http://www.phrap.org/phredphrap/general.html
    Includes cross_match

    Depends on cross_match/1.080812

  735. phred
  736. module name: phred
    version 0.020425.c

    Assigns quality values to DNA sequences
    http://www.phrap.org/phredphrapconsed.html
    Manual: /group/bioinfo/apps/apps/phred-0.020425.c/PHRED.DOC
    Includes daev

  737. Phusion Assembler
  738. module name: phusion-pipeline
    version 2.1c

    Assemble genome sequences from whole genome shotgun(WGS) reads
    http://www.sanger.ac.uk/resources/software/phusion/
    Info: /group/bioinfo/apps/apps/phusion_pipeline_v2.1c/README.1st
    Info: /group/bioinfo/apps/apps/phusion_pipeline_v2.1c/releaseNote_v2.1c
    Info: /group/bioinfo/apps/apps/phusion_pipeline_v2.1c/doc


    Depends on gcc
    Depends on phrap/1.090518

  739. Phusion2
  740. module name: phusion2
    version 3.0

    Genome assembly pipeline based on read clustering
    http://sourceforge.net/projects/phusion2/
    Info: /group/bioinfo/apps/apps/phusion2-3.0/how_to_make_mates


    Depends on gcc

  741. PHYLIP (PHYLogeny Inference Package)
  742. module name: PHYLIP
    version 3.696

    Package of programs for inferring phylogenies (evolutionary trees)
    http://evolution.genetics.washington.edu/phylip.html
    Info: http://evolution.genetics.washington.edu/phylip/phylip.html
    Manual: http://evolution.genetics.washington.edu/phylip/phylipweb.html
    Manual: /group/bioinfo/apps/apps/phylip-3.696/doc

    Depends on gcc

  743. PhyloBayes
  744. module name: PhyloBayes
    version 4.1c

    Phylogenetic reconstruction using infinite mixtures
    http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm
    Manual: http://megasun.bch.umontreal.ca/People/lartillot/www/phylobayes4.1.pdf
    Paper: http://megasun.bch.umontreal.ca/People/lartillot/www/PhyloBayes2009.pdf

    Depends on gsl/2.3
    Depends on gcc

  745. PhyML
  746. module name: phyml
    version 20120412
    Other versions: 20131016

    Estimate maximum-likelihood phylogenies
    http://www.atgc-montpellier.fr/phyml/
    User guide: http://www.atgc-montpellier.fr/phyml/usersguide.php
    Forum: https://groups.google.com/forum/#!forum/phyml-forum
    Includes 20131031.patch
    No support for MPI

    Depends on gcc

  747. Picard
  748. module name: picard-tools
    version 2.9.0
    Other versions: 1.107, 1.108, 1.109, 1.110, 1.111, 1.112, 1.113, 1.114, 1.115, 1.117, 1.118, 1.119, 1.122, 1.123, 1.124, 1.125, 1.126, 1.127, 1.128, 1.129, 1.134, 1.135, 1.63, 1.67, 1.72, 1.74, 1.80, 1.87, 1.88, 1.89, 1.90, 1.91, 1.92, 1.93, 1.94, 1.95, 1.96, 2.0.1, 2.3.0, 2.8.2

    Java based command-line utilities for SAM file manipulation
    http://broadinstitute.github.io/picard/
    FAQ: http://broadinstitute.github.io/picard/faq.html
    Info: http://broadinstitute.github.io/picard/command-line-overview.html
    Issues: https://github.com/broadinstitute/picard/issues

    Picard-tools JAR file is at /group/bioinfo/apps/apps/picard-tools-2.9.0
    Use "PicardCommandLine" command for summary
    Or, use "java [jvm-options] -jar $PICARD/picard.jar [options]" for more control

    Depends on gcc
    Depends on R-bioconductor/3.3.0
    Depends on java/8

  749. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)
  750. module name: PICRUSt
    version 1.0.0

    Predict metagenome functional content from marker gene surveys and full genomes.
    http://picrust.github.io/picrust/
    Forum: https://groups.google.com/group/picrust-users/subscribe?note=1&hl=en&noredirect=true&pli=1
    Tests: /group/bioinfo/apps/apps/PICRUSt-1.0.0/tests

    Depends on gcc
    Depends on tcl
    Depends on igraph
    Depends on HDF5/1.8.14
    Depends on R-bioconductor/3.1.0

  751. PILER (Parsimonious Inference of a Library of Elementary Repeats)
  752. module name: PILER
    version 1.0

    Searches a genome sequence for repetitive elements
    http://www.drive5.com/piler/
    User's Guide: /group/bioinfo/apps/apps/PILER-1.0/manual.pdf

    Depends on gcc
    Depends on PALS
    Depends on muscle

  753. Pilon
  754. module name: Pilon
    version 1.22

    Automated Assembly Improvement and Variant Calling
    http://software.broadinstitute.org/software/pilon/
    Manual: https://github.com/broadinstitute/pilon/wiki

    Start program with:
    java -Xmx16G -jar $PILON_JAR [...other options...]


    Depends on java

  755. Pindel
  756. module name: Pindel
    version 0.2.5b9, 20160729 (github branch downloaded May 9 2017)
    Other versions: May-9-2017, Oct-6-2014

    Detect breakpoints of large deletions, medium sized insertions,
    inversions, tandem duplications and other structural variants at
    single-based resolution from next-gen sequence data
    https://github.com/genome/pindel

    Depends on htslib/1.4

  757. PIPITS
  758. module name: PIPITS
    version 1.3.4

    Pipeline for fungal internal transcribed spacer (ITS) analysis from Illumina sequencers
    https://github.com/hsgweon/pipits

    Depends on biopython/2.7.11
    Depends on fastx
    Depends on vsearch
    Depends on ITSx
    Depends on pear
    Depends on HMMER
    Depends on java
    Depends on rdp_classifier/2.12

  759. platanus
  760. module name: platanus
    version 1.2.4

    A de novo sequence assembler for highly heterozygous diploids from massively parallel shotgun sequencing data
    http://platanus.bio.titech.ac.jp/?page_id=180
    Info: http://platanus.bio.titech.ac.jp/?page_id=2

    Depends on gcc

  761. Platypus
  762. module name: Platypus
    version 0.8.1

    Haplotype-Based Variant Caller For NGS Data
    https://github.com/andyrimmer/Platypus
    http://www.well.ox.ac.uk/platypus

    Depends on biopython/2.7.12

  763. PLEK
  764. module name: PLEK
    version 1.2

    Predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme
    http://www.ibiomedical.net/plek/installation.html

    Depends on biopython/2.7.8

  765. plink
  766. module name: plink
    version 1.07

    Whole genome association analysis toolset
    http://pngu.mgh.harvard.edu/~purcell/plink
    Info: /group/bioinfo/apps/apps/plink-1.07/README.txt

    Depends on gcc

  767. PolyPhen-2 (Polymorphism Phenotyping v2)
  768. module name: PolyPhen
    version 2.2.2r405a

    Predicts possible impact of amino acid substitutions on the structure
    and function of human proteins using straightforward physical and
    evolutionary comparative considerations
    http://genetics.bwh.harvard.edu/pph2/dokuwiki/start
    Docs: http://genetics.bwh.harvard.edu/pph2/dokuwiki/docs

    Will write temp files to $RCAC_SCRATCH/PPH_TEMP
    Temp file directories will be created by loading this module.
    To customize, copy config files with:
    cp -r $PPH/config ~/.pph
    then make changes
    See /group/bioinfo/apps/apps/polyphen-2.2.2r405a/README for more info

    Modified to use zebrafish instead of human data.

    Depends on perl/5.18.1
    Depends on blast/2.2.29+
    Depends on java/6

  769. PoPoolation2
  770. module name: popoolation2
    version 1201

    Compare allele frequencies for SNPs between two or more populations
    https://sourceforge.net/projects/popoolation2/
    Info: https://sourceforge.net/p/popoolation2/wiki/Main/

    The Java JAR is at: $POPOOLATION2_DIR/mpileup2sync.jar

    Depends on perl
    Depends on java
    Depends on samtools
    Depends on bwa

  771. pplacer
  772. module name: pplacer
    version v1.1.alpha13

    Places query sequences on a fixed reference phylogenetic tree to
    maximize phylogenetic likelihood or posterior probability according to
    a reference alignment
    http://matsen.fhcrc.org/pplacer/
    Manual: http://matsen.github.com/pplacer/


    Depends on gcc

  773. Primer Prospector
  774. module name: pprospector
    version 1.0.1

    Pipeline of programs to design and analyze PCR primers
    http://pprospector.sourceforge.net/
    Info: /group/bioinfo/apps/apps/pprospector-1.0.1/ChangeLog

    Depends on biopython/2.7.8
    Depends on ViennaRNA
    Depends on rdp_classifier

  775. Primer3
  776. module name: primer3
    version 2.3.7
    Other versions: 1.1.4, 2.3.4, 2.3.6

    Program for designing PCR primers
    http://primer3.sourceforge.net/
    Manual: /group/bioinfo/apps/apps/primer3-2.3.7/primer3_manual.htm
    Release notes: /group/bioinfo/apps/apps/primer3-2.3.7/release_notes.txt
    Thermodynamic parameter files located in:
    /group/bioinfo/apps/apps/primer3-2.3.7/primer3_config/

    Depends on gcc

  777. PROBer
  778. module name: PROBer
    version 0.1.3-May-27b-2016
    Other versions: 0.1.2, 0.1.3-May-12-2016, 0.1.3-May-27-2016

    Quantitative modeling of transcriptome-wide RNA structure-probing experiments
    https://github.com/pachterlab/PROBer
    Ref: /group/bioinfo/apps/apps/PROBer-0.1.3-May-27b-2016/README.md
    Ref: /group/bioinfo/apps/apps/PROBer-0.1.3-May-27b-2016/README.tools

    Depends on gcc

  779. Prodigal l (Prokaryotic Dynamic Programming Genefinding Algorithm)
  780. module name: prodigal
    version 2.6.3
    Other versions: 2.60

    Microbial (bacterial and archaeal) gene finding program
    https://github.com/hyattpd/prodigal
    http://prodigal.ornl.gov/
    Info: /group/bioinfo/apps/apps/prodigal-2.6.3/README.md
    Changelog: /group/bioinfo/apps/apps/prodigal-2.6.3/CHANGES
    Forum: http://groups.google.com/group/prodigal-discuss

    Depends on gcc

  781. Program to Assemble Spliced Alignments (PASA)
  782. module name: PASA
    version r20140417
    Other versions: 2.0.0, r2012-06-25, r20130605p1, r20130907

    Eukaryotic genome annotation tool
    http://pasa.sourceforge.net
    Info: /group/bioinfo/apps/apps/PASA_r20140417/docs
    Need MySQL database to store results

    Create environment variable $PASACONF with full path to your PASA
    configuration file; e.g.: export PASACONF=~/pasa.conf

    Depends on perl
    Depends on gmap
    Depends on fasta/35
    Depends on seqclean
    Depends on blat

  783. Prokka ("prokaryotic annotation")
  784. module name: Prokka
    version 1.12

    Rapid annotation of prokaryotic genomes
    http://www.vicbioinformatics.com/software.prokka.shtml
    https://github.com/tseemann/prokka

    Depends on perl
    Depends on blast
    Depends on parallel
    Depends on tbl2asn
    Depends on HMMER
    Depends on infernal
    Depends on rnammer
    Depends on signalp
    Depends on prodigal
    Depends on ARAGORN
    Depends on barrnap
    Depends on minced

  785. proovread
  786. module name: proovread
    version 2.14.0

    PacBio hybrid error correction through iterative short read consensus
    https://github.com/BioInf-Wuerzburg/proovread

    Depends on gcc
    Depends on perl
    Depends on blast
    Depends on samtools

  787. ProtTest
  788. module name: prottest
    version 3.3-20130716

    Select best-fit models of protein evolution
    http://code.google.com/p/prottest3/
    Need to copy to your home directory in order to run:
    cp -r $PROTTEST_SRC ~/.
    Follow usage instructions at:
    http://code.google.com/p/prottest3/wiki/Using_Console_Version

    Depends on java

  789. Pscan_ChIP
  790. module name: Pscan_ChIP
    version 1.1

    Find transcription factor-binding site motifs in ChIP-Seq experiments.
    http://159.149.160.51/pscan_chip_dev/
    Help: http://159.149.160.51/pscan_chip_dev/help.html
    Help: /group/bioinfo/apps/apps/Pscan_ChIP-1.1/README.txt

    Depends on gsl

  791. pyfasta
  792. module name: pyfasta
    version 0.5.2

    Fast, memory-efficient, pythonic (and command-line) access to fasta sequence files
    https://pypi.python.org/pypi/pyfasta/

    Depends on biopython/2.7.8

  793. Pyicoteo
  794. module name: Pyicoteo
    version 2.0.7

    Tools for analysing high-throughput sequencing (HTS) data.
    It was mainly developed using Solexa/Illumina mapped reads.
    http://regulatorygenomics.upf.edu/Software/Pyicoteo/index.html

    Depends on biopython/2.7.11

  795. PyQt
  796. module name: PyQt
    version 4.9.4

    Python bindings for Qt application framework
    http://www.riverbankcomputing.co.uk/software/pyqt/intro

    Depends on biopython

  797. pyRAD
  798. module name: pyRAD
    version 3.0.61
    Other versions: 2.15

    Analyze RAD, ddRAD, GBS, paired-end ddRAD and paired-end GBS data sets
    http://dereneaton.com/software/pyrad/

    Depends on biopython/2.7.8
    Depends on muscle
    Depends on vsearch

  799. pysam
  800. module name: pysam
    version 0.7.7
    Other versions: 0.6, 0.7

    Python interface for the SAM/BAM sequence alignment and mapping format
    http://code.google.com/p/pysam/

    Depends on biopython/2.7.3

  801. pyScaf
  802. module name: pyScaf
    version 0.12a

    Genome assembly scaffolding
    https://github.com/lpryszcz/pyScaf

    Depends on biopython/2.7.11
    Depends on LAST

  803. Python with bioinformatics modules
  804. module name: biopython
    version 2.7.2
    Other versions: 2.7.11, 2.7.12, 2.7.3, 2.7.8, 3, 3.5.1

    http://python.org/
    Install info: http://docs.python.org/install/index.html

    Depends on python/2.7.2

  805. PyVCF
  806. module name: PyVCF
    version 0.6.7

    Variant Call Format (VCF) parser for Python
    https://pypi.python.org/pypi/PyVCF

    Depends on biopython/2.7.8

  807. QDD
  808. module name: QDD
    version 3.1.2
    Other versions: 3.1.2b

    Select microsatellite markers and design primers
    http://net.imbe.fr/~emeglecz/qdd.html

    You might need to copy and modify the configuration file before running
    the programs:
    cp -p $QDD_PATH/set_qdd_default.ini $RCAC_SCRATCH
    export QDD_CONF=$RCAC_SCRATCH/set_qdd_default.ini
    edit $RCAC_SCRATCH/set_qdd_default.ini


    Depends on perl
    Depends on RepeatMasker/4.0.5
    Depends on clustalw
    Depends on primer3/2.3.6

  809. QIIME (Quantitative Insights Into Microbial Ecology)
  810. module name: Qiime
    version 1.9.1
    Other versions: 1.6.0, 1.7.0, 1.8.0, 1.9.0, 2, 2-2017.10, 2-2017.11, 2-2017.12, 2-2017.2, 2-2017.8, 2-2017.9

    Comparison and analysis of microbial communities
    http://qiime.org/
    http://qiime.org/documentation_index.html
    Forum: http://forum.qiime.org/
    Info: http://qiime.wordpress.com/
    Config file info: http://qiime.org/install/qiime_config.html
    Parallel QIIME: http://qiime.org/tutorials/parallel_qiime.html

    Includes PhyloToAST (qiime-tools) version 1.1.2
    https://github.com/smdabdoub/phylotoast
    Info: http://qiime-tools.readthedocs.org/

    Includes prepare_taxa_charts.py
    Ref: https://github.com/Xcelris-Labs-Ltd/Publication-ready-taxonomic-charts-from-QIIME

    Depends on gcc
    Depends on tcl
    Depends on igraph
    Depends on R-bioconductor/3.1.2
    Depends on HDF5/1.8.14
    Depends on rdp_classifier/2.2
    Depends on microbiomeutil/r20110519
    Depends on cd-hit/3.1.1
    Depends on mothur/1.25.0
    Depends on clearcut/1.0.9
    Depends on RAxML/standard-5_7_2012
    Depends on infernal/1.0.2
    Depends on muscle/3.8.31
    Depends on usearch/5.2.236
    Depends on usearch/6.1.544
    Depends on rtax/0.984
    Depends on AmpliconNoise/1.27b
    Depends on gsl
    Depends on ghc
    Depends on blast/2.2.22
    Depends on Cytoscape
    Depends on sourcetracker/0.9.5
    Depends on ea-utils

  811. QoRTs
  812. module name: QoRTs
    version 1.1.8
    Other versions: 1.1.2, 1.2.42

    Analysis, quality control, and data management of RNA-Seq datasets
    https://github.com/hartleys/QoRTs
    Vignette: http://hartleys.github.io/QoRTs/doc/QoRTs-vignette.pdf
    Walkthrough: http://hartleys.github.io/JunctionSeq/doc/example-walkthrough.pdf
    Info: http://hartleys.github.io/QoRTs/index.html
    FAQ: http://hartleys.github.io/QoRTs/FAQ.html

    Start java utility using "QoRTs" wrapper script.

    Or, using predefined JAR path:
    java -jar $QoRTs_JAR...

    Depends on R-bioconductor/3.3.0

  813. Qt
  814. module name: Qt
    version 5.6.2
    Other versions: 5.4.0

    Cross-platform application framework
    https://www.qt.io/
    Includes qmake & QtCreator


    Depends on gcc

  815. QTL Cartographer
  816. module name: QTLCart
    version 1.17j

    Suite of programs to map quantitative traits using a map of molecular markers.
    http://statgen.ncsu.edu/qtlcart/
    Example data at /group/bioinfo/apps/apps/QTLCart-1.17j/example

    Depends on gcc
    Depends on gnuplot

  817. Quake
  818. module name: quake
    version 0.3.5

    Fix substitution sequencing errors in Illumina reads with deep coverage
    http://www.cbcb.umd.edu/software/quake/index.html

    Depends on gcc
    Depends on Boost
    Depends on jellyfish
    Depends on R-bioconductor/3.1.0

  819. QualiMap
  820. module name: qualimap
    version 2.2.1
    Other versions: 0.6, 1.0, 2.1.1, 2.1.3

    Graphical and command-line interface for quality control
    of alignment sequencing data
    http://qualimap.bioinfo.cipf.es/
    Manual: /group/bioinfo/apps/apps/qualimap_v2.2.1/QualimapManual.pdf
    Manual: http://qualimap.bioinfo.cipf.es/doc_html/index.html
    Documentation and mailing list on web site
    Need X11 support if you want to use GUI (ssh -X ...)

    Depends on java
    Depends on R-bioconductor/3.1.2

  821. QUAST
  822. module name: quast
    version 3.2
    Other versions: 2.3

    Quality Assessment Tool for Genome Assemblies
    http://bioinf.spbau.ru/QUAST
    Manual: http://quast.bioinf.spbau.ru/manual.html
    Manual: /group/bioinfo/apps/apps/quast-3.2/manual.html

    You need to install QUAST in your home directory as described in the manual.

    Depends on perl/5.20.1
    Depends on biopython/2.7.8
    Depends on java
    Depends on blast

  823. QuEST
  824. module name: quest
    version 2.422
    Other versions: 2.4

    ChIP-Seq data analysis
    http://www.stanford.edu/~valouev/QuEST/QuEST.html
    Forum: http://groups.google.com/group/chipseq

    Depends on gcc
    Depends on perl

  825. Quickmerge
  826. module name: quickmerge
    version 0.2

    A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
    https://github.com/mahulchak/quickmerge

    Depends on MUMmer

  827. Quip
  828. module name: quip
    version 1.1.1-3-g02d3228
    Other versions: 1.1.1

    Compresses next-generation sequencing data in the FASTQ and SAM/BAM formats
    http://www.cs.washington.edu/homes/dcjones/quip/
    Info: https://github.com/dcjones/quip#readme
    or using "man quip"

    Depends on gcc

  829. R with Bioconductor libraries
  830. module name: R-bioconductor
    version 2.15.1
    Other versions: 2.14.1, 2.15.0, 2.15.3, 3.0.2, 3.1.0, 3.1.2, 3.2.3, 3.3.0, 3.3.3, 3.4.0, 3.4.2

    Statistics processing language with bioinformatics libraries
    http://www.r-project.org/
    http://www.bioconductor.org/

    Depends on gcc
    Depends on rhel5libs

  831. Racon
  832. module name: Racon
    version 0.5.0-20180131

    Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
    https://github.com/isovic/racon

    Depends on gcc

  833. RADtools
  834. module name: RADtools
    version 1.2.2

    RAD (Restriction site Associated DNA) Sequencing
    https://www.wiki.ed.ac.uk/display/RADSequencing/Home
    Manual: /group/bioinfo/apps/apps/RADtools-1.2.2/RADmanual.pdf

    Depends on perl

  835. RandA
  836. module name: RandA
    version 1.1.2

    Non-coding RNA profiling based on deep sequencing
    http://ibis.tau.ac.il/RandA/

    Depends on java
    Depends on bwa
    Depends on perl
    Depends on R-bioconductor
    Depends on ea-utils

  837. Randfold
  838. module name: randfold
    version 2.0

    Minimum free energy of folding randomization test software
    http://bioinformatics.psb.ugent.be/software/details/Randfold
    http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/
    randfold version 2 (C version)
    http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/randfold-2.0.tar.gz

    Usage: randfold

    methods:
    -s simple mononucleotide shuffling
    -d dinucleotide shuffling
    -m markov chain 1 shuffling

    Example: randfold -d let7.tfa 999

    Depends on gcc

  839. RAPsearch (Reduced Alphabet based Protein similarity Search)
  840. module name: RAPsearch
    version 2.23
    Other versions: 2.12, 2.16

    Fast protein similarity search
    http://omics.informatics.indiana.edu/mg/RAPSearch2/
    Info: /group/bioinfo/apps/apps/RAPsearch-2.23/readme

    Depends on gcc

  841. Rascaf
  842. module name: Rascaf
    https://github.com/mourisl/Rascaf
    Scaffolding with RNA-seq read alignment

    Depends on gcc

  843. RAxML (standard edition)
  844. module name: RAxML
    version standard-5_7_2012
    Other versions: 8.2.9

    RAxML (Randomized Axelerated Maximum Likelihood)
    Maximum Likelihood based inference of large phylogenetic trees
    http://sco.h-its.org/exelixis/software.html
    Manual: http://sco.h-its.org/exelixis/countManual7.0.4.php
    Info: /group/bioinfo/apps/apps/RAxML-standard-5_7_2012/README
    Forum: https://groups.google.com/forum/?fromgroups#!forum/raxml

    Depends on gcc

  845. Ray
  846. module name: ray
    version 2.3.1b
    Other versions: 2.1.0, 2.2.0, 2.3.0, 2.3.0-zlib, 2.3.1

    Parallel genome assemblies for parallel DNA sequencing
    http://denovoassembler.sourceforge.net/index.html
    Manual: http://denovoassembler.sourceforge.net/manual.html
    Manual: /group/bioinfo/apps/apps/ray-2.3.1b/MANUAL_PAGE.txt
    Docs: /group/bioinfo/apps/apps/ray-2.3.1b/Documentation
    Forum: http://denovoassembler.sourceforge.net/mailing-list.html
    Max k-mer length = 256
    Includes libz support for uncompressing fastq.gz files

    Depends on gcc
    Depends on openmpi

  847. REAGO
  848. module name: REAGO
    version 1.1

    An assembly tool for 16S ribosomal RNA recovery from metagenomic data
    https://github.com/chengyuan/reago-1.1

    Might need to copy contents of "cm" directory from /group/bioinfo/apps/apps/reago-1.1 to your working directory.

    Depends on biopython/2.7.11
    Depends on infernal/1.1.1
    Depends on GenomeTools

  849. REAPR (Recognising Errors in Assemblies using Paired Reads)
  850. module name: REAPR
    version 1.0.16

    Evaluates the accuracy of a genome assembly using mapped paired end reads
    http://www.sanger.ac.uk/resources/software/reapr/

    Depends on perl
    Depends on R-bioconductor
    Depends on Artemis

  851. RECON
  852. module name: RECON
    version 1.08
    Other versions: 1.07

    Indentifies repeat families from biological sequences
    http://selab.janelia.org/recon.html
    RepeatModeler version mentioned on:
    http://www.repeatmasker.org/RepeatModeler.html
    Docs: /group/bioinfo/apps/apps/RECON-1.08/00README
    Demos: /group/bioinfo/apps/apps/RECON-1.08/Demos/

    Depends on perl

  853. Redundans
  854. module name: Redundans
    version 0.13a-try3
    Other versions: 0.13a, 0.13a-try2, 2016-11-18

    Assembly pipeline for heterozygous/polymorphic genomes
    https://github.com/Gabaldonlab/redundans

    Feb 1 2017 release

    Depends on biopython/2.7.11
    Depends on perl

  855. RepARK
  856. module name: RepARK
    version 1.2

    Repetitive motif detection by Assembly of Repetitive K-mers
    https://github.com/PhKoch/RepARK
    Docs: /group/bioinfo/apps/apps/RepARK-1.2/README

    Depends on jellyfish/1.1.11
    Depends on velvet/1.2.07

  857. RepeatMasker
  858. module name: RepeatMasker
    version 4.0.7
    Other versions: 3.3.0, 4.0.0, 4.0.1, 4.0.2, 4.0.3, 4.0.5, 4.0.6

    Screens DNA sequences for interspersed repeats and low complexity
    http://www.repeatmasker.org/
    Manual: http://www.repeatmasker.org/webrepeatmaskerhelp.html
    Manual: /group/bioinfo/apps/apps/RepeatMasker-4.0.7/repeatmasker.help
    FAQ: http://www.repeatmasker.org/faq.html

    Dfam database version Dfam_2.0
    RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127

    Installed Search Engines:
    1. Default = RMBlast (NCBI BLAST with RepeatMasker extensions)
    2. CrossMatch
    3. HMMER & DFAM

    Genomic Datasets:
    http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html

    Depends on trf
    Depends on perl
    Depends on cross_match
    Depends on blast/2.2.28+
    Depends on HMMER

  859. RepeatModeler
  860. module name: RepeatModeler
    version 1.0.9
    Other versions: 1.0.7, 1.0.8

    De-novo repeat family identification and modeling package
    http://www.repeatmasker.org/RepeatModeler.html
    Manual: /group/bioinfo/apps/apps/RepeatModeler-1.0.9/README

    Depends on RepeatMasker
    Depends on RepeatScout
    Depends on RECON

  861. RepeatScout
  862. module name: RepeatScout2
    version 1.0.5

    This is probably a fork of RepeatScout
    https://github.com/DobzhanskyCenter/RepeatScout2
    Info: /group/bioinfo/apps/apps/RepeatScout2-1.0.5/README
    The -freq file can only have two fields per line

    Depends on perl
    Depends on trf
    Depends on nseg

  863. RGT (Regulatory Genomics Toolbox)
  864. module name: RGT
    version 0.10.0

    http://www.regulatory-genomics.org/
    Integrative analysis of high throughput regulatory genomics data
    Includes THOR to detect and analyze differential peaks in ChIP-seq data
    http://www.regulatory-genomics.org/thor-2/basic-intrstruction/

    Depends on gcc

  865. riboFrame
  866. module name: riboFrame
    version 1.0

    Improved method for microbial taxonomy profiling from non targeted metagenomics
    http://bioserver2.sbsc.unifi.it/bioinfo/riboframe.html
    Example data in /group/bioinfo/apps/apps/riboFrame-1.0/sample

    Depends on HMMER
    Depends on rdp_classifier
    Depends on R-bioconductor/3.3.0

  867. RIGERJ
  868. module name: rigerj
    version 2.0.1

    Java implementation of RIGER and other gene enrichment methods, useful for RNAi and CRISPR screen analysis
    https://github.com/broadinstitute/rigerj
    Run using:
    java -jar $RIGERJ_JAR ...


    Depends on java

  869. rMATS
  870. module name: rMATS
    version 3.0.9

    Multivariate Analysis of Transcript Splicing (MATS)
    http://rnaseq-mats.sourceforge.net/index.html
    Forum: https://groups.google.com/forum/#!forum/rmats-user-group

    Depends on biopython/2.7.8
    Depends on samtools/0.1.19
    Depends on tophat/1.4.1
    Depends on bowtie/0.12.8

  871. RMBlast
  872. module name: rmblast
    version 2.2.28
    Other versions: 1.2, 2.2.27

    RepeatMasker compatible version of the standard NCBI BLAST
    http://www.repeatmasker.org/RMBlast.html

    Depends on blast/2.2.28+

  873. RNA-SeQC
  874. module name: RNA-SeQC
    version 1.1.8

    Computes a series of quality control metrics for RNA-seq data
    http://www.broadinstitute.org/cancer/cga/rna-seqc
    Info: http://www.broadinstitute.org/cancer/cga/rnaseqc_run
    Docs: http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/RNA-SeQC_Help_v1.1.2.pdf

    Use "RNA-SeQC-cmd" command for summary
    Or, use "java [jvm-options] -jar $RNA_SeQC/RNA-SeQC.jar [options]" for more control

    Depends on java
    Depends on bwa

  875. RNAhybrid
  876. module name: RNAhybrid
    version 2.1.2

    Find minimum free energy hybridization of a long and a short RNA
    http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
    Manual: man RNAhybrid
    Manual: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid?id=rnahybrid_manual_manual

    Depends on gcc

  877. RNAmmer
  878. module name: rnammer
    version 1.2

    Predicts ribosomal RNA genes in prokaryotic genome sequences
    http://www.cbs.dtu.dk/services/RNAmmer/
    Info: man rnammer

  879. rnaQUAST
  880. module name: rnaQUAST
    version 1.4.0

    Evaluate quality of transcriptome assemblies using reference genome and gene database
    http://bioinf.spbau.ru/en/rnaquast
    https://academic.oup.com/bioinformatics/article/32/14/2210/1743439/rnaQUAST-a-quality-assessment-tool-for-de-novo
    Manual: http://spades.bioinf.spbau.ru/rnaquast/release1.4.0/manual.html

    Depends on gcc
    Depends on biopython/2.7.12
    Depends on blat
    Depends on gmap
    Depends on blast
    Depends on kentUtils
    Depends on HMMER

  881. Rockhopper
  882. module name: Rockhopper
    version 2.0.3

    Analysis of bacterial RNA-seq data
    User Guide: http://cs.wellesley.edu/~btjaden/Rockhopper/user_guide.html
    FAQ: http://cs.wellesley.edu/~btjaden/Rockhopper/FAQ.html
    Need X11 support for program to run (ssh -X)
    Use "Rockhopper" command to start GUI with default settings

    Depends on java/7

  883. ROOT
  884. module name: ROOT
    version 6.02.03-rhel6

    Data analysis framework
    https://root.cern.ch/drupal/
    Binary-download; production version
    Requires gcc >= 4.8

    Depends on gcc/4.8.2

  885. RSEG
  886. module name: rseg
    version 0.4.9

    Analyze ChIP-Seq data
    http://smithlabresearch.org/software/rseg/
    Manual: http://smithlabresearch.org/wp-content/uploads/rseg_manual-v0.4.9.pdf

    Depends on gcc

  887. RSEM
  888. module name: rsem
    version 1.3.0
    Other versions: 1.1.19, 1.1.20, 1.1.21, 1.2.0, 1.2.11, 1.2.12, 1.2.15, 1.2.18, 1.2.25, 1.2.30, 1.2.7

    RSEM (RNA-Seq by Expectation-Maximization)
    http://deweylab.github.io/RSEM/
    Forum: https://groups.google.com/forum/#!forum/rsem-users

    Depends on gcc
    Depends on R-bioconductor/3.3.3
    Depends on perl
    Depends on bowtie
    Depends on bowtie2
    Depends on STAR

  889. RSeQC
  890. module name: RSeQC
    version 2.6.4
    Other versions: 2.6.3

    Evaluate high throughput sequence data especially RNA-seq data
    http://rseqc.sourceforge.net/

    Depends on biopython/2.7.12
    Depends on R-bioconductor/3.4.0

  891. RStudio Desktop Open Source Edition
  892. module name: RStudio
    version 1.1.383
    Other versions: 1.0.143, 1.1.240, 1.1.244

    Integrated Development Environment for R
    https://www.rstudio.com/products/RStudio/
    Notes: https://www.rstudio.com/products/rstudio/release-notes/
    Notes: https://blog.rstudio.com/2017/10/09/rstudio-v1.1-released/

    Depends on gcc
    Depends on R/3.4.2
    Depends on Qt/5.4.0
    Depends on Boost/1.63.0
    Depends on gstreamer
    Depends on java

  893. rtax
  894. module name: rtax
    version 0.984
    Other versions: 0.983

    Taxonomic classification of short paired-end sequence reads from the
    16S ribosomal RNA gene.
    http://dev.davidsoergel.com/trac/rtax/
    Docs: http://dev.davidsoergel.com/trac/rtax/wiki/QuickStart
    Forum: http://dev.davidsoergel.com/trac/rtax/discussion/1
    Used by QIIME; ref: http://qiime.org/tutorials/rtax.html


    Depends on perl
    Depends on usearch

  895. Ruby
  896. module name: ruby
    version 2.3.0
    Other versions: 2.0.0-p195

    Programming language
    http://www.ruby-lang.org/en/
    Documentation: http://www.ruby-lang.org/en/documentation/

    Depends on gcc

  897. Sailfish
  898. module name: sailfish
    version 0.9.2
    Other versions: 0.10.0

    Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
    http://www.cs.cmu.edu/~ckingsf/software/sailfish/
    https://github.com/kingsfordgroup/sailfish
    Manual: http://sailfish.readthedocs.io/en/master/

    Depends on gcc

  899. Salmon
  900. module name: salmon
    version 0.8.2
    Other versions: 0.8.0

    Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
    https://github.com/COMBINE-lab/salmon
    Manual: http://salmon.readthedocs.io/en/latest/

    Depends on gcc

  901. samstat
  902. module name: samstat
    version 1.08

    Displaying sequence statistics for next generation sequencing
    http://samstat.sourceforge.net/

    Depends on gcc

  903. SAMtools
  904. module name: samtools
    version 1.6
    Other versions: 0.1.16, 0.1.18, 0.1.19, 0.1.8, 0.2.0-devel-29-July-2014, 1.0, 1.1, 1.2, 1.3, 1.3.1, 1.4, 1.5

    Utilities for manipulating alignments in the SAM format
    http://www.htslib.org/
    Man pages for: samtools, wgsim
    Manual: http://www.htslib.org/doc/
    Support: http://www.htslib.org/support/#lists

    Depends on htslib/1.6
    Depends on bcftools/1.6

  905. SCaFoS (Selection, Concatenation and Fusion of Sequences)
  906. module name: scafos
    version 1.2.5

    Phylogenetic analysis tool
    http://megasun.bch.umontreal.ca/Software/scafos/scafos.html
    Manual: http://megasun.bch.umontreal.ca/Software/scafos/scafos_help.html
    Needs X11 support to run

    Depends on perl
    Depends on tree-puzzle

  907. segemehl
  908. module name: segemehl
    version 0.2.0
    Other versions: 0.1.7

    Short read mapping with gaps
    http://www.bioinf.uni-leipzig.de/Software/segemehl/
    Manual: /group/bioinfo/apps/apps/segemehl-0.2.0/manual.pdf

    Depends on gcc
    Depends on gsl/2.3

  909. SeqAlto
  910. module name: seqalto
    version 0.5-r123
    Other versions: 0.5-r117

    Fast and accurate read aligner for moderately long Illumina reads
    http://www.stanford.edu/group/wonglab/seqalto/
    Manual: http://www.stanford.edu/group/wonglab/seqalto/manual.shtml
    Info: /group/bioinfo/apps/apps/seqalto-0.5-r123/README.txt

  911. seqbuster
  912. module name: seqbuster
    version 44

    Small RNA analysis of deep sequencing data
    http://code.google.com/p/seqbuster/
    Documentation on web site
    Copy /group/bioinfo/apps/apps/seqbuster-44 to a private directory and work from it

    Depends on BEDTools
    Depends on java
    Depends on R-bioconductor
    Depends on blast
    Depends on ViennaRNA

  913. SeqPrep
  914. module name: SeqPrep
    version 27-Aug-2013

    Merge overlapping, paired end Illumina reads into a single read and/or trim adapters.
    https://github.com/jstjohn/SeqPrep

    Depends on gcc

  915. seqtk
  916. module name: seqtk
    version 1.0-r82b
    Other versions: 1.0-r68e

    Parses FASTA and FASTQ files
    https://github.com/ndaniel/seqtk
    Info: /group/bioinfo/apps/apps/seqtk-1.0-r82b/README.md

    Depends on gcc

  917. Sequence Cleaner
  918. module name: seqclean
    version 2011-02-22

    Automated trimming and validation of ESTs or other DNA sequences
    http://compbio.dfci.harvard.edu/tgi/software/
    http://sourceforge.net/projects/seqclean/

    Depends on perl
    Depends on blast/2.2.26

  919. SequenceServer
  920. module name: SequenceServer
    version 1.0.7

    Server with web front end for BLAST+
    http://www.sequenceserver.com/
    Documentation: http://www.sequenceserver.com/doc
    Forum: https://groups.google.com/forum/#!forum/sequenceserver

    Probably doesn't work

    Depends on ruby/2.3.0
    Depends on blast

  921. SeqyClean
  922. module name: seqyclean
    version 1.3.13

    Clean Roche 454 and Illumina NGS data
    http://cores.ibest.uidaho.edu/software/seqyclean
    Manual: /group/bioinfo/apps/apps/seqyclean-1.3.13/man/SeqyClean_UserManual.pdf

    Depends on gcc

  923. SGA String Graph Assembler
  924. module name: SGA
    version 0.10.12

    De novo sequence assembler using string graphs
    http://genome.cshlp.org/content/22/3/549
    https://github.com/jts/sga
    FAQ: https://github.com/jts/sga/wiki/FAQ

    Depends on pysam

  925. ShellCheck
  926. module name: shellcheck
    version 0.3.8

    A shell script static analysis tool
    https://github.com/koalaman/shellcheck

    Depends on haskell-platform

  927. SHORE (Short Read)
  928. module name: SHORE
    version 0.9.3

    Mapping and analysis pipeline for short read data produced on the Illumina platform.
    http://1001genomes.org/software/shore.html
    Manual: http://shore.sourceforge.net/wiki/
    Info: /group/bioinfo/apps/apps/shore-0.9.3/share

    Depends on Boost
    Depends on gsl
    Depends on xz
    Depends on GenomeMapper

  929. SHOREmap
  930. module name: SHOREmap
    version 3.4
    Other versions: 3.0

    Fast and accurate identification of causal mutations in plants
    http://bioinfo.mpipz.mpg.de/shoremap/index.html

    Depends on DISLIN
    Depends on xz
    Depends on SHORE

  931. SHRiMP
  932. module name: SHRiMP
    version 2.2.3
    Other versions: 2.2.2

    SHort Read Mapping; aligning genomic reads against a target genome
    http://compbio.cs.toronto.edu/shrimp/
    Info in /group/bioinfo/apps/apps/SHRiMP-2.2.3/README

    Depends on gcc

  933. SICER
  934. module name: SICER
    version 1.1

    A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    http://home.gwu.edu/~wpeng/Software.htm
    Manual: /group/bioinfo/apps/apps/SICER-1.1/README.pdf
    Forum: http://groups.google.com/group/sicer-users

    Depends on biopython/2.7.8

  935. SignalP
  936. module name: signalp
    version 4.1c
    Other versions: 4.1b

    Predicts the presence and location of signal peptide cleavage sites in
    amino acid sequences from different organisms
    http://www.cbs.dtu.dk/services/SignalP/
    http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp
    License: /group/bioinfo/apps/apps/signalp-4.1c/signalp-4.1.licence.txt
    Manual page: "man signalp"
    Default MAX_ALLOWED_ENTRIES changed from 10,000 to 2,000,000

  937. SiLiX
  938. module name: silix
    version 1.2.8

    ultra fast SIngle LInkage Clustering of Sequences
    http://lbbe.univ-lyon1.fr/Overview.html
    Info: man pages for silix and silixx

    Depends on gcc

  939. SInC
  940. module name: SInC
    version 2014-01-20

    An accurate & fast error-model based simulator for SNPs, Indel & CNVs
    https://sourceforge.net/projects/sincsimulator/

    Depends on gcc

  941. SMRT Analysis
  942. module name: smrtanalysis
    version 2.3.0.140936

    http://www.pacb.com/products-and-services/analytical-software/smrt-analysis/
    https://github.com/PacificBiosciences/SMRT-Analysis
    Genomic analysis from PacBio
    Info: https://github.com/PacificBiosciences/SMRT-Analysis/wiki

    Important info in http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Pipe-Reference-Guide.pdf

    To use interactively, first run "smrtshell" command.

    To use in batch bash job, first run "source $SMRT_ROOT/current/etc/setup.sh"

    This is not compatible with other software modules!

  943. SNAP
  944. module name: snap
    version 0.15
    Other versions: 0.13.11, 0.13.4

    Scalable Nucleotide Alignment Program
    http://snap.cs.berkeley.edu/
    Info: http://snap.cs.berkeley.edu/#documentation
    Info: /group/bioinfo/apps/apps/snap-0.15/snap-0.15-manual.pdf
    Info: /group/bioinfo/apps/apps/snap-0.15/snap-0.15-quickstart.pdf

  945. SNAP (Semi-HMM-based Nucleic Acid Parser)
  946. module name: SNAP
    version 2013-02-16

    Gene prediction tool.
    http://korflab.ucdavis.edu/software.html
    Info: /group/bioinfo/apps/apps/SNAP-2013-02-16/00README

    Depends on gcc

  947. snpEff and snpSift
  948. module name: snpEff
    version 4.3p
    Other versions: 3.3F, 3.6, 4.0e, 4.1, 4.1d, 4.2, 4.3

    Genetic variant annotation and effect prediction toolbox
    http://snpeff.sourceforge.net/index.html
    Manual: http://snpeff.sourceforge.net/SnpEff_manual.html

    Start program with:
    java -jar $snpEff_root/snpEff.jar ...

    Might need to change configuration options. Make copy of config file
    from /group/bioinfo/apps/apps/snpEff-4.3p/snpEff.config and modify as needed.
    Then, reference your modified config file as:
    java -jar $snpEff_root/snpEff.jar -c path/to/modified/snpEff.config ...

    See manual for more information

    Also includes SnpSift
    See: http://snpeff.sourceforge.net/SnpSift.html
    Start program with:
    java -jar $snpEff_root/SnpSift.jar ...

    Also includes ClinEff version 1.0g:
    See: http://www.dnaminer.com/clineff.html
    Start program with:
    java -jar $clinEff_root/ClinEff.jar ...


    Depends on java

  949. SNPhylo
  950. module name: SNPhylo
    version 20140701

    Pipeline to generate a phylogenetic tree from SNP data
    http://chibba.pgml.uga.edu/snphylo/

    Depends on PHYLIP
    Depends on biopython/2.7.8
    Depends on R-bioconductor/3.1.2
    Depends on muscle

  951. SOAPaligner
  952. module name: SOAPaligner
    version 2.21

    SOAP (Short Oligonucleotide Analysis Package)
    Short oligonucleotide alignment
    http://soap.genomics.org.cn/soapaligner.html
    Info: http://soap.genomics.org.cn/soapaligner.html#commopt2

  953. SOAPdenovo
  954. module name: SOAPdenovo
    version 240
    Other versions: 1.05

    SOAP (Short Oligonucleotide Analysis Package)
    Assemble Illumina GA short reads
    http://soap.genomics.org.cn/soapdenovo.html
    Info: http://soap.genomics.org.cn/soapdenovo.html#comm2

  955. SOAPdenovo-Trans
  956. module name: SOAPdenovo-Trans
    version 1.03

    SOAP (Short Oligonucleotide Analysis Package)
    De novo transcriptome assembler
    http://soap.genomics.org.cn/SOAPdenovo-Trans.html
    http://sourceforge.net/projects/soapdenovotrans/
    Info: /group/bioinfo/apps/apps/SOAPdenovo-Trans-1.03/MANUAL
    Example data: /group/bioinfo/apps/apps/SOAPdenovo-Trans-1.03/example

    Depends on gcc

  957. SOAPec
  958. module name: SOAPec
    version 2.03
    Other versions: 2.02

    Corrects sequencing errors based on kmer frequency spectrum (KFS)
    Info: /group/bioinfo/apps/apps/SOAPec_bin_v2.03/ReadMe
    Info: /group/bioinfo/apps/apps/SOAPec_bin_v2.03/NEWS

  959. SOAPfuse
  960. module name: SOAPfuse
    version 1.26

    Genome-wide detection of fusion transcripts from paired-end RNA-Seq data
    http://soap.genomics.org.cn/soapfuse.html

    To run SOAPfuse; you need to make your own copy of the program and data files.
    Those files are located in /group/bioinfo/apps/apps/SOAPfuse-v1.26
    Read /group/bioinfo/apps/apps/SOAPfuse-v1.26/README.Purdue for more information
    You will need to download and install index files

    Depends on perl

  961. SOAPfusion
  962. module name: SOAPfusion
    version 0.3
    Other versions: 0.2

    Genome-wide discovery of gene fusion events from RNA-seq data.
    http://soap.genomics.org.cn/SOAPfusion.html

    To run SOAPfusion; you probably need to make your own copy of the program and data files.
    Those files are located in /group/bioinfo/apps/apps/SOAPfusion-v0.3
    Read /group/bioinfo/apps/apps/SOAPfusion-v0.3/README.Purdue for more information
    You will need to download and install index files

  963. SOAPsplice
  964. module name: SOAPsplice
    version 1.8

    SOAP (Short Oligonucleotide Analysis Package)
    Detection of splice junction sites from RNA-Seq
    http://soap.genomics.org.cn/soapsplice.html
    Info: http://soap.genomics.org.cn/soapsplice.html#commopt2

  965. SOAPsv
  966. module name: SOAPsv
    version 1.02

    SOAP (Short Oligonucleotide Analysis Package)
    Detecting structural variation by whole genome de novo assembly
    http://soap.genomics.org.cn/SOAPsv.html
    Manual at /group/bioinfo/apps/apps/SOAPsv-1.02/SOAPSV-Pipeline-Doc.pdf
    Manual at http://soap.genomics.org.cn/down/SOAPSV-Pipeline-Doc.doc

  967. SolexaQA
  968. module name: SolexaQA
    version 1.1.13

    Calculate quality data from Illumnia/Solexa FASTQ files
    http://solexaqa.sourceforge.net/
    Manual at /group/bioinfo/apps/apps/SolexaQA-1.1.13/SolexaQA_v.1.13_Manual.txt

    Depends on matrix2png
    Depends on R-bioconductor

  969. Some RHEL 5 shared libaries
  970. module name: rhel5libs
    version 1.0

    This is a copy of the following shared libraries from RHEL5 RPMs
    that are bundled with RCAC RHEL 5 community clusters.
    - blas-3.0-38.el5
    - libgfortran-4.1.2-52.el5
    - mysql-5.0.95-1.el5_7.1
    - openssl-0.9.8e-22.el5
    - tk-8.4.13-5.el5_1.1
    - db4-4.3.29-10.el5_5.2
    - expat-1.95.8-11.el5_8

    Depends on gcc

  971. SortMeRNA
  972. module name: SortMeRNA
    version 2.1b
    Other versions: 2.1

    Biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads
    http://bioinfo.lifl.fr/RNA/sortmerna/
    Manual: /group/bioinfo/apps/apps/sortmerna-2.1b/manual.pdf

    Depends on gcc

  973. SourceTracker
  974. module name: sourcetracker
    version 0.9.5

    Bayesian approach to estimating the proportion of a novel community
    that comes from a set of source environments
    http://sourceforge.net/projects/sourcetracker/

  975. SPAdes
  976. module name: spades
    version 3.9.1
    Other versions: 2.2.1, 2.3.0, 3.0.0, 3.1.0, 3.10.1, 3.1.1, 3.11.0, 3.11.1, 3.5.0, 3.5.0-p1, 3.5.0-p2, 3.6.0, 3.6.1, 3.6.2, 3.7.0, 3.8.0, 3.9.0

    Genome assembler for multicell and single-cell MDA bacteria
    http://bioinf.spbau.ru/spades
    Manual: http://spades.bioinf.spbau.ru/release3.9.1/manual.html
    Manual: /group/bioinfo/apps/apps/spades-3.9.1/share/spades/manual.html


    Depends on gcc
    Depends on biopython/2.7.11

  977. Sparc
  978. module name: Sparc
    version 2016-04-22

    Sparsity-based consensus algorithm for long erroneous sequencing reads
    https://github.com/yechengxi/Sparc

    This probably doesn't work

    Depends on blasr
    Depends on biopython/2.7.8

  979. SparseAssembler
  980. module name: SparseAssembler
    version 2015-12-08

    Sparse k-mer Graph for Memory Efficient Genome Assembly
    https://sites.google.com/site/sparseassembler/
    https://sourceforge.net/projects/sparseassembler/
    Info: /group/bioinfo/apps/apps/SparseAssembler-2015-12-08/Manual.txt

  981. sparsehash
  982. module name: sparsehash
    version 2.0.2
    Other versions: 2.0.1, 2.0.2-intel

    An extremely memory-efficient hash_map implementation
    http://code.google.com/p/sparsehash/?redir=1
    Info: /group/bioinfo/apps/apps/sparsehash-2.0.2/share/doc/sparsehash-2.0.2
    Info: http://sparsehash.googlecode.com/svn/trunk/doc/index.html

    Depends on gcc

  983. SplAdder
  984. module name: spladder
    version Apr-09-2015

    Splice Adder; augments genome annotation using RNA-Seq alignment data.
    http://raetschlab.org/suppl/spladder
    This is the Python language version, not the MATLAB one.

    Depends on biopython/2.7.8

  985. SpliceGrapher
  986. module name: splicegrapher
    version 0.2.4
    Other versions: 0.1.0, 0.2.0

    Create splice graphs from RNA-Seq data, guided by gene models and EST data
    http://splicegrapher.sourceforge.net/index.html
    Tutorial at http://splicegrapher.sourceforge.net/tutorial.html
    Manual: http://splicegrapher.sourceforge.net/userguide.html
    Manual: /group/bioinfo/apps/apps/SpliceGrapher-0.2.4/doc/userguide.pdf

    Depends on biopython/2.7.8

  987. SQUID
  988. module name: squid
    version 1.9g

    C function library for sequence analysis
    http://eddylab.org/software.html
    Documentation on web site and man pages

    Depends on gcc

  989. SRA Toolkit
  990. module name: sra-toolkit
    version 2.8.2-1
    Other versions: 2.1.6, 2.3.5, 2.4.2, 2.5.1, 2.5.2, 2.5.7, 2.8.0

    Tools for using data in the INSDC Sequence Read Archives
    http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
    Help: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
    Help: /group/bioinfo/apps/apps/sratoolkit-2.8.2-1/help

    Includes taxid2tsa.pl and taxid2wgs.pl for TSA & WGS data searches
    Ref: ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS/README_BLASTWGS.txt


    Depends on perl

  991. SSPACE
  992. module name: SSPACE
    version 3.0
    Other versions: 2.0

    Scaffolding pre-assembled contigs using paired-read data
    http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
    http://www.baseclear.com/bioinformatics-tools
    Manual: /group/bioinfo/apps/apps/SSPACE-STANDARD-3.0/manual.pdf
    Tutorial: /group/bioinfo/apps/apps/SSPACE-STANDARD-3.0/tutorial.pdf
    Paper: http://bioinformatics.oxfordjournals.org/content/27/4/578.abstract

    Depends on gcc

  993. SSPACE-LongRead
  994. module name: SSPACE-LongRead
    version 1-1

    Scaffolding pre-assembled contigs using long reads
    http://www.baseclear.com/lab-products/bioinformatics-tools/sspace-longread/

  995. Stacks
  996. module name: stacks
    version 1.35
    Other versions: 0.998, 0.999, 0.9991, 0.9995, 0.9996, 0.9999, 0.99991, 0.99993, 0.99996, 0.99997, 1.01, 1.02, 1.04, 1.05, 1.06, 1.08, 1.09, 1.10, 1.12, 1.13, 1.17, 1.18, 1.19, 1.20, 1.21, 1.29, 1.34

    Pipeline for building loci out of a set of short-read sequenced samples
    http://catchenlab.life.illinois.edu/stacks/
    FAQ: http://catchenlab.life.illinois.edu/stacks/faq.php

    You will need to configure a MySQL database to view results.

    Depends on gcc
    Depends on perl
    Depends on samtools/0.1.19

  997. Stampy
  998. module name: stampy
    version 1.0.26
    Other versions: 1.0.22, 1.0.23

    Mapping of short reads from Illumina sequencing machines onto a reference genome
    http://www.well.ox.ac.uk/project-stampy
    Info: /group/bioinfo/apps/apps/stampy-1.0.26/README.txt

    Depends on biopython/2.7.8
    Depends on bwa

  999. Stanford Network Analysis Platform (SNAP)
  1000. module name: SNAP_library
    version 1.10

    C++ library for analysis and manipulation of large networks
    http://snap.stanford.edu/index.html
    Docs: http://snap.stanford.edu/snap/doc.html
    Info in /group/bioinfo/apps/apps/Snap-1.10/README.txt
    Examples in /group/bioinfo/apps/apps/Snap-1.10/examples
    Tutorial in /group/bioinfo/apps/apps/Snap-1.10/tutorials
    Hint: Make a copy of everthing in /group/bioinfo/apps/apps/Snap-1.10
    then work in your copy of the tutorials directory

    Depends on gcc
    Depends on gnuplot

  1001. STAR
  1002. module name: STAR
    version 2.5.3a
    Other versions: 2.4.0j, 2.4.0k, 2.4.1d, 2.4.2a, 2.5.0c, 2.5.1b, 2.5.2b

    RNA-seq aligner
    https://github.com/alexdobin/STAR
    Manual: /group/bioinfo/apps/apps/STAR-2.5.3a/doc/STARmanual.pdf
    Info: /group/bioinfo/apps/apps/STAR-2.5.3a/README.md
    Info: /group/bioinfo/apps/apps/STAR-2.5.3a/RELEASEnotes.md
    Info: /group/bioinfo/apps/apps/STAR-2.5.3a/CHANGES.md

    Depends on gcc

  1003. storm
  1004. module name: storm
    version 0.20

    Object Relational Mapper for the Python programming language.
    Python module
    https://launchpad.net/storm

    Depends on biopython/2.7.3

  1005. StringTie
  1006. module name: stringtie
    version 1.3.3
    Other versions: 1.0.1, 1.0.2

    Transcript assembly and quantification for RNA-Seq
    http://ccb.jhu.edu/software/stringtie/
    Info: /group/bioinfo/apps/apps/stringtie-1.3.3/README

    Depends on gcc

  1007. Structure
  1008. module name: Structure
    version 2.3.4

    Use multi-locus genotype data to investigate population structure
    http://pritchardlab.stanford.edu/structure.html
    Manual at /group/bioinfo/apps/apps/structure-2.3.4/doc/structure_doc.pdf
    Need X11 support to see graphics
    Use "structure-gui" to start GUI/X11 version
    Use "structure" for command line version

    Depends on java
    Depends on CLUMPP
    Depends on distruct

  1009. SUMATRA and SUMACLUST
  1010. module name: sumatra
    version 1.0.00

    Fast and exact comparison and clustering of sequences
    http://metabarcoding.org/sumatra
    Manual: /group/bioinfo/apps/apps/sumatra-1.0.00/sumatra_sumaclust_user_manual.pdf

    Depends on gcc

  1011. SUPPA
  1012. module name: SUPPA
    version 2.2.0

    Study splicing across multiple conditions
    https://bitbucket.org/regulatorygenomicsupf/suppa

    Depends on biopython/3.5.1

  1013. SWIG
  1014. module name: swig
    version 3.0.8

    SWIG is a compiler that integrates C and C++ with other languages
    http://www.swig.org
    Info: /group/bioinfo/apps/apps/swig-3.0.8/README

    Depends on gcc

  1015. T-COFFEE
  1016. module name: T-COFFEE
    version 9.03r1318

    Multiple Sequence Alignment Tools
    http://www.tcoffee.org/Projects/tcoffee/

    Just includes the t_coffee program

    Depends on gcc
    Depends on perl

  1017. T-lex
  1018. module name: tlex
    version 2.0

    Computational pipeline that detects presence and/or absence of
    annotated individual transposable elements
    License and download: http://petrov.stanford.edu/Tlex_scripts/
    Manual at http://petrov.stanford.edu/cgi-bin/Tlex_manual.html

    Depends on fastagrep
    Depends on cross_match
    Depends on blat
    Depends on SHRiMP
    Depends on maq
    Depends on RepeatMasker

  1019. tabix
  1020. module name: tabix
    version 0.2.6

    Generic indexer for TAB-delimited genome position files
    http://samtools.sourceforge.net/
    Info: http://samtools.sourceforge.net/tabix.shtml
    or using "man tabix"

    Depends on gcc

  1021. Target Finder
  1022. module name: TargetFinder
    version 1.7
    Other versions: 1.6

    Plant small RNA target prediction tool
    https://github.com/carringtonlab/TargetFinder
    Info: /group/bioinfo/apps/apps/TargetFinder-1.7/README

    Depends on perl
    Depends on fasta/35

  1023. TASR pipeline
  1024. module name: TASR
    version 1.1

    TASR (Transposon Annotation using Small RNAs)
    http://sourceforge.net/projects/tasr-pipeline/
    Info: /group/bioinfo/apps/apps/TASR-1.1/README
    Info: /group/bioinfo/apps/apps/TASR-1.1/TASR_tutorial
    License: /group/bioinfo/apps/apps/TASR-1.1/LICENSE
    Citation: http://nar.oxfordjournals.org/content/early/2015/03/26/nar.gkv257.full

    Start program with command "TASR"

    Need to specify location of usearch7 program which is:
    -usearchv /group/bioinfo/apps/apps/usearch-7.0.1090/bin/usearch7


    Depends on perl
    Depends on blast
    Depends on bowtie2/2.2.3
    Depends on trf
    Depends on usearch/7
    Depends on silix

  1025. TASSEL
  1026. module name: TASSEL
    version 5.2.9
    Other versions: 5.2.36

    Association mapping of complex traits in diverse samples.
    http://www.maizegenetics.net/#!tassel/c17q9
    Manual: https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual
    Forum: http://groups.google.com/group/tassel
    Needs X11 support for GUI:
    https://www.rcac.purdue.edu/compute/carter/guide/#accounts_login_x11

    Depends on java/8

  1027. TBB (Intel Threading Building Blocks)
  1028. module name: tbb
    version 2017_20161128oss

    C++ template library for task parallelism
    https://www.threadingbuildingblocks.org/

    CPPFLAGS=-I/group/bioinfo/apps/apps/tbb2017_20161128oss/include
    LDFLAGS=-L/group/bioinfo/apps/apps/tbb2017_20161128oss/lib/intel64/gcc4.7

    Depends on gcc

  1029. tbl2asn
  1030. module name: tbl2asn
    version 25.3
    Other versions: 22.9, 24.9

    Automates the submission of sequence records to GenBank
    ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/
    Info: /group/bioinfo/apps/apps/tbl2asn-25.3/tbl2asn.txt

    Also includes table2asn_GFF version 1.19.259


    Depends on gcc

  1031. Tcl/Tk (Tool Command Language)
  1032. module name: tcl
    version 8.6.1

    Dynamic programming language
    Includes Tk GUI widget platform
    http://www.tcl.tk/
    Manuals: http://www.tcl.tk/doc/

    Depends on gcc

  1033. Tedna
  1034. module name: tedna
    version 1.2.2-mid-k91
    Other versions: 1.2.2, 1.2.2-fast-k91, 1.2.2-slow-k91

    Lightweight de novo transposable element assembler
    It assembles the transposable elements directly from the raw reads.
    https://urgi.versailles.inra.fr/Tools/Tedna
    Documentation: https://urgi.versailles.inra.fr/content/download/2962/25436/file/doc.pdf
    Documentation: /group/bioinfo/apps/apps/tedna-1.2.2-mid-k91/doc.pdf

    Built using C++/mid hash implementation and
    max k-mer size of 91

    Depends on gcc

  1035. TeX Live
  1036. module name: texlive
    version 2013

    TeX document production system
    http://www.tug.org/texlive/

    Depends on gcc

  1037. The GNU C Library (glibc)
  1038. module name: glibc
    https://www.gnu.org/software/libc/
    Core libraries for GNU/Linux systems

  1039. tidyp
  1040. module name: tidyp
    version 1.04

    Validate HTML
    http://tidyp.com/

    Depends on gcc

  1041. TMHMM
  1042. module name: tmhmm
    version 2.0c

    Prediction of transmembrane helices in proteins
    http://www.cbs.dtu.dk/services/TMHMM/
    http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
    License: /group/bioinfo/apps/apps/tmhmm-2.0c/tmhmm-2.0c.licence.txt
    Manual: /group/bioinfo/apps/apps/tmhmm-2.0c/TMHMM2.0.html

    Depends on perl
    Depends on gnuplot
    Depends on netpbm-progs

  1043. TopHat
  1044. module name: tophat
    version 2.1.1
    Other versions: 1.3.2, 1.3.3, 1.4.0, 1.4.1, 2.0.0, 2.0.10, 2.0.11, 2.0.13, 2.0.14, 2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.9, 2.1.0

    Spliced read mapper for RNA-Seq
    http://ccb.jhu.edu/software/tophat/index.shtml
    Manual: http://ccb.jhu.edu/software/tophat/manual.shtml
    Forum: https://groups.google.com/forum/#!forum/tuxedo-tools-users

    According to TopHat release notes: "TopHat has entered a low
    maintenance, low support stage as it is now largely superseded by
    HISAT2 which provides the same core functionality (i.e. spliced
    alignment of RNA-Seq reads), in a more accurate and much more
    efficient way."

    Use "module load hisat2" to use that software


    Depends on gcc
    Depends on zlib
    Depends on bowtie2/2.2.9
    Depends on bowtie
    Depends on blast

  1045. Tracer
  1046. module name: Tracer
    version 1.6

    Analyze trace files generated by Bayesian MCMC runs of BEAST, MrBayes, LAMARC, etc.
    http://tree.bio.ed.ac.uk/software/tracer/

    Need X11 support to run. Consult:
    https://www.rcac.purdue.edu/knowledge/halstead/accounts/all#accounts_login_x11

    Depends on java

  1047. trans-ABySS
  1048. module name: trans-abyss
    version 1.5.5
    Other versions: 1.3.2, 1.5.1, 1.5.3

    de novo assembly of RNA-Seq data using ABySS
    http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
    https://github.com/bcgsc/transabyss

    Tutorial: /group/bioinfo/apps/apps/transabyss-1.5.5/TUTORIAL.txt
    Support: http://groups.google.com/group/trans-abyss

    Depends on abyss/1.5.2-maxk64
    Depends on biopython/2.7.8
    Depends on blat/35
    Depends on bowtie2
    Depends on gmap
    Depends on samtools/1.3

  1049. TransDecoder
  1050. module name: TransDecoder
    version 3.0.1
    Other versions: 2.0.1, 2.1.0, 3.0.0-beta

    Find Coding Regions Within Transcripts
    http://transdecoder.github.io/

    Depends on perl

  1051. TransposonPSI
  1052. module name: TransposonPSI
    version 08222010

    Use PSI-Blast to Mine (Retro-)Transposon ORF Homologies
    http://transposonpsi.sourceforge.net/

    Depends on perl
    Depends on blast/2.2.26

  1053. Transrate
  1054. module name: transrate
    version 1.0.1

    de-novo transcriptome assembly quality analysis
    http://hibberdlab.com/transrate/index.html
    Mailing list: https://groups.google.com/forum/#!forum/transrate-users
    Bug tracker: https://github.com/Blahah/transrate/issues
    Live chat: https://gitter.im/Blahah/transrate

    Depends on gcc

  1055. Tree Puzzle
  1056. module name: tree-puzzle
    version 5.2

    Maximum likelihood analysis for nucleotide, amino acid, and two-state data
    http://www.tree-puzzle.de/
    Manual: http://www.tree-puzzle.de/tree-puzzle.pdf
    Manual: /group/bioinfo/apps/apps/tree-puzzle-5.2/doc/tree-puzzle.pdf

    Depends on gcc

  1057. TreeFix
  1058. module name: TreeFix
    version 1.1.10

    Statistically Informed Gene Tree Error Correction Using Species Trees
    https://www.cs.hmc.edu/~yjw/software/treefix/

    Depends on biopython/2.7.12

  1059. TRF (Tandem Repeats Finder)
  1060. module name: trf
    version 4.09
    Other versions: 4.04

    Locate and display tandem repeats in DNA sequences
    http://tandem.bu.edu/trf/trf.html

  1061. TrimAl
  1062. module name: trimal
    version 1.2r59
    Other versions: 1.4.1

    Removes spurious or poorly aligned regions from a multiple sequence alignment
    http://trimal.cgenomics.org/

    Depends on gcc

  1063. TrimGalore
  1064. module name: TrimGalore
    version 0.4.4

    Adapter and quality trimming for FastQ files, with extra functionality for RRBS data
    https://github.com/FelixKrueger/TrimGalore
    Manual at https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
    Manuals in /group/bioinfo/apps/apps/TrimGalore-0.4.4/Docs

    Depends on fastqc
    Depends on cutadapt

  1065. Trimmomatic
  1066. module name: trimmomatic
    version 0.36
    Other versions: 0.17, 0.20, 0.22, 0.30, 0.32, 0.33

    A flexible read trimming tool for Illumina NGS data
    http://www.usadellab.org/cms/index.php?page=trimmomatic
    Manual: /group/bioinfo/apps/apps/trimmomatic-0.36/manual.pdf
    Use "trimmomatic" to start the program

    Depends on java

  1067. Trinity
  1068. module name: trinity
    version 2.5.1
    Other versions: 2.0.2, 2.0.3, 2.0.6, 2.1.0, 2.1.1, 2.2.0, 2.3.2, 2.4.0, b20140127, b20140128, b20140316, b20140323, beta, r2012-01-25, r2012-03-17, r2012-04-27, r2012-05-18, r2012-06-08, r2012-10-05, r2013-02-15, r2013-02-16, r2013-02-25, r2013_08_14, r20131110, r20140413, r20140413p1, r20140717, r20150110beta

    RNA-Seq De novo Assembly
    https://github.com/trinityrnaseq/trinityrnaseq/wiki
    Forum: https://groups.google.com/forum/#!forum/trinityrnaseq-users
    Ref: /group/bioinfo/apps/apps/trinityrnaseq-2.5.1/Changelog.txt

    For parallel processing with PBS support; see:
    /group/bioinfo/apps/apps/trinityrnaseq-2.5.1/util/PBS/README

    If storing output in Lustre filesystem, configure output directory
    with "lfs setstripe -c 1" and submit job with "#PBS -l software=trinity"
    as described in http://www.rcac.purdue.edu/news/detail.cfm?NewsID=555

    Depends on gcc
    Depends on java
    Depends on perl
    Depends on samtools
    Depends on bowtie2
    Depends on R
    Depends on PASA
    Depends on rsem
    Depends on express

  1069. Trinity (development version)
  1070. module name: trinity-dev
    version 2165
    Other versions: 1697

    RNA-Seq De novo Assembly
    http://trinityrnaseq.sourceforge.net/
    Manual: http://trinityrnaseq.sourceforge.net/advanced_trinity_guide.html
    FAQ: http://trinityrnaseq.sourceforge.net/trinity_faq.html
    Forum: http://sourceforge.net/mailarchive/forum.php?forum_name=trinityrnaseq-users
    Ref: /group/bioinfo/apps/apps/trinityrnaseq_dev-2165/Release.Notes
    Ref: /group/bioinfo/apps/apps/trinityrnaseq_dev-2165/docs

    Depends on gcc
    Depends on java
    Depends on perl
    Depends on samtools
    Depends on bowtie
    Depends on R-bioconductor

  1071. Trinotate
  1072. module name: trinotate
    version r20131110
    Other versions: 2.0.2, 3.0.1, 3.1.1

    Transcriptome functional annotation and analysis
    http://trinotate.sourceforge.net/

    Requires sequence databases:
    - /group/bioinfo/apps/apps/Trinotate_r20131110/data/uniprot_sprot.fasta.gz
    - /group/bioinfo/apps/apps/Trinotate_r20131110/data/Pfam-A.hmm.gz
    Copy these files and create the databases as described in step 2 in
    http://trinotate.sourceforge.net/

    SQLite database with swissprot-related annotation information
    - /group/bioinfo/apps/apps/Trinotate_r20131110/data/Trinotate.sqlite.gz

    Depends on trinity
    Depends on blast
    Depends on signalp
    Depends on tmhmm
    Depends on rnammer
    Depends on HMMER

  1073. tRNAscan-SE
  1074. module name: tRNAscan-SE
    version 1.3.1

    Search for tRNA genes in genomic sequence
    http://lowelab.ucsc.edu/tRNAscan-SE/
    Info: man tRNAscan-SE

  1075. uclust
  1076. module name: uclust
    version 1.2.22q

    Extreme high-speed sequence clustering, alignment and database search
    http://www.drive5.com/uclust/uclust_userguide_1_1_579.html
    Forum: http://www.drive5.com/mlist.html

  1077. UNAFold
  1078. module name: unafold
    version 3.8

    RNA and DNA secondary structure prediction mainly by using thermodynamic methods
    http://mfold.rna.albany.edu/?q=node/60
    man pages available
    docs: http://mfold.rna.albany.edu/?q=unafold-man-pages

    Depends on gcc

  1079. Unicycler
  1080. module name: Unicycler
    version 0.4.4

    Assembly pipeline for bacterial genomes
    https://github.com/rrwick/Unicycler
    Documentation: /group/bioinfo/apps/apps/Unicycler-0.4.4/docs
    Sample data: /group/bioinfo/apps/apps/Unicycler-0.4.4/sample_data


    Depends on gcc
    Depends on spades
    Depends on Racon
    Depends on Pilon
    Depends on samtools
    Depends on bowtie2
    Depends on blast

  1081. usearch
  1082. module name: usearch
    version 5.2.236
    Other versions: 5.2.32, 6, 6.1.544, 7, 7.0.1090, 7.0.959, 8, 8.0.1517, 8.0.1623, 8.1.1861, 9, 9.0.2132, 9.2.64

    High-throughput biological sequence analysis
    http://drive5.com/usearch/
    License: http://www.drive5.com/usearch/license32.html
    Docs: /group/bioinfo/apps/apps/usearch-5.2.236/UsearchUserGuide5.2.pdf
    Docs: http://drive5.com/usearch/manual/
    32-bit version only; used by QIIME


  1083. USeq
  1084. module name: USeq
    version 8.4.0

    Analysis of next generation signature sequencing data
    http://useq.sourceforge.net/
    Usage: http://useq.sourceforge.net/usage.html
    Forum: https://lists.sourceforge.net/lists/listinfo/useq-users

    Depends on java
    Depends on R-bioconductor

  1085. util-linux
  1086. module name: util-linux
    version 2.25.2

    Miscellaneous system utilities
    https://packages.debian.org/stable/util-linux
    https://www.kernel.org/pub/linux/utils/util-linux/

    Depends on gcc

  1087. vcflib
  1088. module name: vcflib
    version 03-Dec-2015

    Utilities and C++ library for parsing and manipulating VCF files
    https://github.com/ekg/vcflib
    Info: /group/bioinfo/apps/apps/vcflib-03-Dec-2015/README.md

    Depends on gcc
    Depends on perl
    Depends on R-bioconductor/3.1.0

  1089. VCFtools
  1090. module name: vcftools
    version 0.1.14
    Other versions: 0.1.11, 0.1.12, 0.1.12a, 0.1.12b, 0.1.13, 0.1.9

    Validate, merge, compare and calculate basic population genetic statistics from VCF files
    https://vcftools.github.io/index.html
    Info: https://vcftools.github.io/examples.html
    Info: man vcftools

    Depends on htslib

  1091. Velvet
  1092. module name: velvet
    version 1.2.10
    Other versions: 1.2.03, 1.2.07, 1.2.10-kmer151

    Sequence assembler for very short reads
    http://www.ebi.ac.uk/~zerbino/velvet/
    Manual: /group/bioinfo/apps/apps/velvet_1.2.10/doc/Manual.pdf
    Includes colorspace support
    Build parameters:
    - MAXKMERLENGTH=99
    - CATEGORIES=4
    - OPENMP=1

    Depends on gcc

  1093. VelvetOptimizer
  1094. module name: VelvetOptimiser
    version 2.2.4

    Automatically optimize parameters for the Velvet assembler
    http://bioinformatics.net.au/software.velvetoptimiser.shtml
    Manual: http://www.vicbioinformatics.com/velvetoptimiser.manual.txt
    Manual: /group/bioinfo/apps/apps/VelvetOptimiser-2.2.4/README

    Depends on velvet
    Depends on perl

  1095. ViennaRNA
  1096. module name: ViennaRNA
    version 2.3.5
    Other versions: 1.8.5, 2.0.7, 2.1.1, 2.2.4

    RNA Secondary Structure Prediction and Comparison
    http://www.tbi.univie.ac.at/~ronny/RNA/
    Manual: /group/bioinfo/apps/apps/ViennaRNA-2.3.5/share/doc/ViennaRNA/RNAlib-2.3.5.pdf
    Documentation on web site and man pages

    Depends on perl/5.20.1
    Depends on graphviz

  1097. Vmatch
  1098. module name: Vmatch
    version 2.3.0
    Other versions: 2.2.4

    Large scale sequencer analysis software
    http://www.vmatch.de/
    Manual: /group/bioinfo/apps/apps/vmatch-2.3.0/virtman.pdf
    Manual: http://www.vmatch.de/virtman.pdf

    Depends on gcc
    Depends on perl

  1099. vsearch
  1100. module name: vsearch
    version 2.4.3
    Other versions: 1.4.7, 2.0.2

    Metagenomics tool; free replacement for usearch
    https://github.com/torognes/vsearch
    Manual: /group/bioinfo/apps/apps/vsearch-2.4.3/doc/vsearch_manual.pdf
    or use "man vsearch"


  1101. WebLogo
  1102. module name: weblogo
    version 2.8.2

    Generates sequence logos, which illustrate
    amino acid or nucleic acid multiple sequence alignment
    http://weblogo.berkeley.edu/

    Depends on perl

  1103. WIGGLER (a.k.a. align2rawsignal)
  1104. module name: WIGGLER
    version 2.0

    Creates genome-wide raw or normalized signal tracks from aligned sequencing reads (BAM/tagAlign)
    https://code.google.com/p/align2rawsignal/wiki/README
    March 2013 update

    Includes scripts for generating binary unique mappability tracks for
    each contig/chromosome. Need to run them from somewhere else:
    cp -rp /group/bioinfo/apps/apps/align2rawsignal-2.0/map /some/where/else


    Depends on MCR
    Depends on samtools/1.0
    Depends on bowtie

  1105. Wise2 (includes genewise)
  1106. module name: wise
    version 2.4.1
    Other versions: 2.2.3-rc7

    Align proteins or protein HMMs to DNA
    http://www.ebi.ac.uk/~birney/wise2/
    Docs: /group/bioinfo/apps/apps/wise2.4.1/docs
    Run it online at http://www.ebi.ac.uk/Tools/psa/genewise/


    Depends on gcc

  1107. XZ Utils
  1108. module name: xz
    version 5.2.3
    Other versions: 5.0.5

    Data compression (xz, lzma) software with high compression ratio
    http://tukaani.org/xz/
    Info: /group/bioinfo/apps/apps/xz-5.2.3/share/doc/xz/
    man pages available


    Depends on gcc

  1109. YASS
  1110. module name: yass
    version 1.14

    Genomic similarity search tool for nucleic (DNA/RNA) sequences
    http://bioinfo.lifl.fr/yass/
    Use "man yass" for usage info

    Depends on gcc

  1111. zlib
  1112. module name: zlib
    version 1.2.8
    Other versions: 1.2.11, 1.2.7

    Free compression library
    http://www.zlib.net/
    man -s3 zlib

    Depends on gcc
Updated: Thu Feb 1 10:24:23 2018
  • No labels