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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 1.9.0-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-nosparsehash, 1.9.0-maxk96, 1.9.0-nompi-maxk64, maxk128, maxk256, maxk64, maxk96

    Assembly By Short Sequences
    http://www.bcgsc.ca/platform/bioinfo/software/abyss
    Info in /group/bioinfo/apps/apps/abyss-1.9.0-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 Boost
    Depends on openmpi/1.8.1_gcc-4.7.2

  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 52415
    Other versions: 40969, 41634, 42667, 48686

    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-52415/share/doc/allpathslg/AllPaths-LG_Manual.pdf

    Depends on gcc
    Depends on gmp
    Depends on picard-tools

  9. AMOS
  10. 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

  11. AmpliconNoise
  12. module name: rdp_classifier
    version 2.4
    Other versions: 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

  13. ANNOVAR
  14. 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

  15. Apache Ant
  16. 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

  17. Argtable
  18. module name: argtable
    version 2-13

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

    Depends on gcc

  19. Artemis
  20. 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
    Depends on java

  21. Aspera Connect Client including ascp
  22. 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

  23. AUGUSTUS
  24. module name: AUGUSTUS
    version 3.2.1
    Other versions: 2.7, 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

  25. Automatically Tuned Linear Algebra Software (ATLAS)
  26. module name: ATLAS
    version 3.10.1

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

    Depends on gcc

  27. BAMStats
  28. 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

  29. bamtools
  30. 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

  31. bamUtil
  32. 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

  33. Batman
  34. 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

  35. BayeScan
  36. 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

  37. BBMap/BBTools
  38. module name: BBTools
    version 35.85
    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

    Short read aligner, and other bioinformatic tools
    http://sourceforge.net/projects/bbmap/
    Info at /group/bioinfo/apps/apps/BBMap-35.85/docs
    Guides at /group/bioinfo/apps/apps/BBMap-35.85/docs/guides
    In particular, see /group/bioinfo/apps/apps/BBMap-35.85/docs/guides/BBMapGuide.txt

    Depends on java
    Depends on samtools

  39. bcftools
  40. module name: bcftools
    version 1.3

    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
    Depends on htslib/1.3

  41. bcl2fastq
  42. module name: bcl2fastq
    version 1.8.4
    Other versions: 1.8.3, 2.16.0.10

    illumina BCL2FASTQ Conversion Software
    BCL conversion and demultiplexing of both unzipped and zipped bcl files
    http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html
    Manual: /group/bioinfo/apps/apps/bcl2fastq-1.8.4/docs/bcl2fastq/BCL2FASTQ_1_8_4_LetterBooklet_UG_15038058B.pdf
    Notes: /group/bioinfo/apps/apps/bcl2fastq-1.8.4/docs/bcl2fastq/BCL2FASTQ_1_8_4_Software_Release_Notes.pdf
    License: /group/bioinfo/apps/apps/bcl2fastq-1.8.4/bcl2fastq2-v2-16-EULA.pdf

    Depends on gcc
    Depends on perl/5.16.0

  43. BEAGLE
  44. 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

  45. bedops
  46. module name: bedops
    version 2.0
    Other versions: 1.2.5

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

    Depends on biopython/2.7.3

  47. BEDTools
  48. module name: BEDTools
    version 2.25.0
    Other versions: 2.16.2, 2.17.0, 2.20.1, 2.21.0

    A flexible suite of utilities for comparing genomic features
    https://github.com/arq5x/bedtools2/releases
    Manual: http://bedtools.readthedocs.org/en/latest/
    Forum at http://groups.google.com/group/bedtools-discuss

    Depends on gcc
    Depends on samtools

  49. Bellman's GAP compiler
  50. module name: gapc
    version 2014.10.07

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

    Depends on gcc

  51. BESST
  52. 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

  53. BFAST
  54. 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

  55. Bioinformatics utilities
  56. 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

  57. biom-format
  58. 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

  59. biotoolbox
  60. 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

  61. Bismark
  62. module name: bismark
    version 0.14.5
    Other versions: 0.10.1, 0.14.2

    Map bisulfite converted sequence reads and determine cytosine methylation states
    http://www.bioinformatics.babraham.ac.uk/projects/bismark/
    Manual: /group/bioinfo/apps/apps/bismark_v0.14.5/Bismark_User_Guide.pdf

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

  63. BLASR
  64. module name: blasr
    version 1.3.1

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

    Depends on HDF5

  65. blast2html
  66. 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

  67. BLAT
  68. module name: blat
    version 35
    Other versions: 34

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

    Depends on gcc

  69. BLESS
  70. 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

  71. boost
  72. module name: Boost
    version 1_54_0
    Other versions: 1.54.0

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

    Depends on gcc

  73. Bowtie
  74. module name: bowtie
    version 1.1.2
    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

    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-1.1.2/MANUAL
    Tutorial: http://bowtie-bio.sourceforge.net/tutorial.shtml
    Tutorial: /group/bioinfo/apps/apps/bowtie-1.1.2/TUTORIAL

  75. Bowtie2
  76. module name: bowtie2
    version 2.2.8
    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

    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/bowtie2-2.2.8/MANUAL
    FAQ: http://bowtie-bio.sourceforge.net/bowtie2/faq.shtml

    Depends on gcc
    Depends on perl

  77. BRAKER1
  78. module name: BRAKER
    version 1.8

    Pipeline for unsupervised RNA-Seq-based genome annotation
    http://bioinf.uni-greifswald.de/augustus/downloads/
    Info: /group/bioinfo/apps/apps/BRAKER-1.8/README.braker
    Example data: $BRAKER_PATH/example

    Need to set $AUGUSTUS_CONFIG_PATH to be a path in which the program can write files.

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

  79. BreakDancer
  80. 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

  81. bwa
  82. module name: bwa
    version 0.7.12
    Other versions: 0.5.9, 0.6.1, 0.6.2, 0.7.10, 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-0.7.12/README.md
    Info: /group/bioinfo/apps/apps/bwa-0.7.12/doc/README.md
    Info: /group/bioinfo/apps/apps/bwa-0.7.12/doc/NEWS.md

    Depends on gcc
    Depends on perl

  83. CAP3
  84. 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

  85. CASAVA
  86. 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

  87. CD-HIT
  88. module name: cd-hit
    version 4.6.1-2012-08-27-openmp
    Other versions: 3.1.1, 4.6-2012-04-25, 4.6.1-2012-08-27

    Clustering and comparing protein or nucleotide sequences
    http://weizhong-lab.ucsd.edu/cd-hit/
    https://code.google.com/p/cdhit/
    Docs: http://weizhong-lab.ucsd.edu/cd-hit/doc.php
    Info: /group/bioinfo/apps/apps/cd-hit-v4.6.1-2012-08-27-openmp/doc
    User Guide: /group/bioinfo/apps/apps/cd-hit-v4.6.1-2012-08-27-openmp/cd-hit-user-guide.pdf

    Depends on gcc

  89. cdbtools
  90. 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

  91. CEAS
  92. 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

  93. CEGMA (Core Eukaryotic Genes Mapping Approach)
  94. 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

  95. Celera Assembler
  96. 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

  97. Censor
  98. 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+

  99. CentroidFold
  100. 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

  101. CFITSIO
  102. module name: CFITSIO
    version 3.370

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

    Depends on gcc

  103. CIRCexplorer
  104. module name: CIRCexplorer
    version 1.1.3

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

    Depends on biopython/2.7.8
    Depends on tophat
    Depends on STAR
    Depends on BEDTools
    Depends on samtools

  105. Circos
  106. module name: Circos
    version 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

  107. clearcut
  108. 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

  109. CleaveLand
  110. 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

  111. CLUMPP
  112. 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

  113. Clustal Omega
  114. module name: clustalo
    version 1.2.1
    Other versions: 1.1.0

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

    Depends on argtable

  115. ClustalW2
  116. module name: clustalw
    version 2.1

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

    Depends on gcc

  117. CNVer
  118. 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

  119. CNVnator
  120. 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

  121. consed
  122. 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

  123. Control-FREEC
  124. 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

  125. corset
  126. 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

  127. cortex_var
  128. 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

  129. CRI-MAP Improved
  130. 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

  131. CRISP
  132. 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

  133. cross_match
  134. 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)

  135. Cufflinks
  136. 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

  137. cURL and libcurl
  138. 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

  139. cutadapt
  140. module name: cutadapt
    version 1.9.1
    Other versions: 1.1a, 1.1b

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

    Depends on biopython/2.7.8

  141. Cytoscape
  142. 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

  143. DANPOS
  144. 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

  145. DBG2OLC
  146. 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

  147. DeconSeq
  148. 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

  149. deepTools
  150. module name: deeptools
    version 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

  151. DELLY
  152. 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

  153. DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation)
  154. 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

  155. DIALIGN-TX
  156. module name: DIALIGN-TX
    version 1.0.2

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

    Depends on perl
    Depends on gcc

  157. DIAMOND
  158. module name: diamond
    version 0.7.9
    Other versions: 0.6.12, 0.7.1, 0.7.8

    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-0.7.9/README.rst

    Includes Aug 21 2015 NCBI nr database data at $DIAMONDDB/nr.dmnd
    Includes Aug 21 2015 NCBI refseq_protein data at $DIAMONDDB/refseq_protein.dmnd

  159. diffReps
  160. module name: diffReps
    version 1.55.4

    Finding differential chromatin modification sites from ChIP-seq data
    https://code.google.com/p/diffreps/

    Depends on perl/5.20.1

  161. DiNuP
  162. 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

  163. DISCOVAR
  164. 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

  165. DISCOVAR de novo
  166. 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

  167. DISLIN
  168. module name: DISLIN
    version 10.5

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

    Probably need X11 support

    Depends on gcc

  169. distruct
  170. 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

  171. dna-bison
  172. 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 openmpi/1.8.1_gcc-4.7.2
    Depends on biopython/2.7.8
    Depends on bowtie2
    Depends on R-bioconductor/3.1.0

  173. DOTS-Finder
  174. 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

  175. ea-utils
  176. 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

  177. EDGE-pro
  178. 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

  179. elinks
  180. 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

  181. EMBOSS
  182. module name: EMBOSS
    version 6.6.0
    Other versions: 6.4.0, 6.5.7

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

    Includes Jemboss; need X11 support

    Depends on gcc
    Depends on java
    Depends on rhel5libs

  183. EMMAX
  184. 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

  185. Exonerate
  186. module name: exonerate
    version 2.2.0

    Generic tool for sequence alignment
    http://www.ebi.ac.uk/~guy/exonerate/
    Use "man exonerate" for more info

    Depends on gcc

  187. expat
  188. module name: expat
    version 2.1.0

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

    Depends on gcc

  189. eXpress
  190. 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

  191. FASconCAT
  192. 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

  193. FASTA
  194. 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

  195. Fasta Utilities
  196. 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

  197. FastaGrep
  198. 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

  199. fastq_screen
  200. 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

  201. FastQC
  202. module name: fastqc
    version 0.11.2
    Other versions: 0.10.0, 0.10.1

    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

  203. FastTree
  204. 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/

  205. FASTX-Toolkit
  206. module name: fastx
    version 0.0.13.2
    Other versions: 0.0.13

    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

  207. FLASH (Fast Length Adjustment of SHort reads)
  208. 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

  209. flexbar
  210. 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

  211. Fold-Grammars
  212. 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

  213. FragGeneScan
  214. module name: FragGeneScan
    version 1.19
    Other versions: 1.16

    Finds (fragmented) genes in short reads
    http://omics.informatics.indiana.edu/FragGeneScan/
    Example data in /group/bioinfo/apps/apps/FragGeneScan-1.19/example
    Training data in /group/bioinfo/apps/apps/FragGeneScan-1.19/train

    Depends on gcc

  215. FusionCatcher
  216. module name: FusionCatcher
    version 0.99.5a
    Other versions: 0.99.4c

    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 83

    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/2.5.0c
    Depends on bowtie2/2.2.6
    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

  217. GAEMR (Genome Assembly Evaluation, Metrics and Reporting)
  218. 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

  219. GAM-NGS
  220. 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

  221. GapCloser
  222. 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

  223. GapFiller
  224. 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

  225. GATK (Genome Analysis Toolkit; Full version)
  226. module name: GATK
    version 3.5
    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, nightly-2015-08-23

    Analyse next-generation resequencing data
    http://www.broadinstitute.org/gatk/
    Forum: http://gatkforums.broadinstitute.org/
    GenomeAnalysisTK.jar file at /group/bioinfo/apps/apps/GATK-3.5
    Run the script "GenomeAnalysisTK" to use it.
    License terms at /group/bioinfo/apps/apps/GATK-3.5/LICENSE
    Info: http://gatkforums.broadinstitute.org/discussion/6495/version-highlights-for-gatk-version-3-5

    Depends on java

  227. GATK Queue
  228. module name: GATK-Queue
    version 3.5
    Other versions: 3.2.2, 3.3.0, 3.4.0, 3.4.46

    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-3.5
    Run the script "Queue" to use it.
    License terms at /group/bioinfo/apps/apps/GATK-Queue-3.5/LICENSE

    Depends on GATK/3.4.46

  229. GATK-Lite (Genome Analysis Toolkit; Public version)
  230. 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

  231. GEM (GEnome Multi-tool) Library
  232. 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

  233. geneid
  234. 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

  235. GeneMark-ES/ET
  236. module name: GeneMark
    version 4.32
    Other versions: 2.5m

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

    Depends on perl

  237. Genepop
  238. 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

  239. GenePRIMP (Gene PRediction IMprovement Pipeline)
  240. 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

  241. GeneWise
  242. module name: genewise
    version 2.2.3-rc7

    Comparisons of bio polymers
    http://www.ebi.ac.uk/Tools/Wise2/doc_wise2.html
    Docs: /group/bioinfo/apps/apps/wise-2.2.3-rc7/docs


    Depends on gcc

  243. GenomeMapper
  244. 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

  245. GenomeThreader
  246. module name: GenomeThreader
    version 1.6.5

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

    Depends on Vmatch

  247. GenomeTools
  248. module name: GenomeTools
    version 1.4.1
    Other versions: 1.3.9

    Bioinformatics tools collection including LTRharvest
    http://genometools.org/
    Manuals: /group/bioinfo/apps/apps/gt-1.4.1/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

    Depends on gcc

  249. Genovo
  250. 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

  251. Glasgow Haskell Compiler
  252. 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

  253. GLIMMER
  254. 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

  255. GlimmerHMM
  256. 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

  257. GMAP and GSNAP
  258. module name: gmap
    version 2014-12-21-amd
    Other versions: 2012-01-11, 2012-04-27, 2012-11-27, 2014-02-20, 2014-12-16v2, 2014-12-16v2-amd

    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-2014-12-21-amd/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

  259. GMP
  260. 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

  261. GNU Autoconf
  262. module name: autoconf
    version 2.69

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

    Depends on m4

  263. GNU Automake
  264. module name: automake
    version 1.14

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

    Depends on autoconf

  265. GNU Libtool
  266. module name: libtool
    version 2.4.2

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

  267. GNU M4
  268. module name: m4
    version 1.4.17

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

  269. GNU MPFR
  270. 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

  271. GNU parallel
  272. module name: parallel
    version 20150622
    Other versions: 20130122, 20130722, 20150522

    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

  273. GNU Scientific Library (GSL)
  274. module name: gsl
    version 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

  275. Gnuplot
  276. module name: gnuplot
    version 4.6.6
    Other versions: 4.6.1, 4.6.2

    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

  277. gpg-error
  278. 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

  279. GREAT (Genomic Regions Enrichment of Annotations Tool)
  280. 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

  281. GS FLX
  282. 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

  283. gtextutils
  284. module name: libgtextutils
    version 0.6

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

    Depends on gcc

  285. gVCFtools
  286. module name: gvcftools
    version 0.15

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

    Depends on gcc

  287. hapsembler
  288. 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

  289. Haskell Platform
  290. 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

  291. HDF5
  292. module name: HDF5
    version 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/

  293. HMMER
  294. 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

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

    Suite of tools for Motif Discovery and next-gen sequencing analysis
    http://homer.salk.edu/homer/

    Depends on perl
    Depends on samtools
    Depends on blat
    Depends on R-bioconductor
    Depends on weblogo

  297. HTSeq
  298. module name: htseq
    version 0.6.1
    Other versions: 0.5.3p3

    Analysing high-throughput sequencing data with Python
    http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
    http://pypi.python.org/pypi/HTSeq

    Depends on biopython/2.7.3

  299. htslib
  300. module name: htslib
    version 1.3

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

    Depends on gcc
    Depends on perl
    Depends on curl
    Depends on gsl

  301. hyb
  302. 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

  303. i-ADHoRe
  304. 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 openmpi/1.8.1_gcc-4.7.2

  305. IDBA
  306. module name: idba
    version 1.1.0
    Other versions: 0.19

    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
    IDBA, IDBA-UD, IDBA-Hybrid and IDBA-Tran all in one package

    Depends on gcc
    Depends on blat

  307. IDBA-UD
  308. 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

  309. igraph
  310. module name: igraph
    version 0.7.1

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

    Depends on gcc

  311. IGV (Integrative Genomics Viewer)
  312. 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

  313. IGV Tools
  314. 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

  315. IMAGE
  316. 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

  317. ImageMagick
  318. 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

  319. indelMINER
  320. module name: indelMINER
    version 1.0

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

    Depends on gcc

  321. Infernal
  322. module name: infernal
    version 1.0.2

    Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
    http://infernal.janelia.org/
    Manual: /group/bioinfo/apps/apps/infernal-1.0.2/Userguide.pdf
    Inf: /group/bioinfo/apps/apps/infernal-1.0.2/documentation/


    Depends on gcc

  323. iNPS
  324. 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

  325. InterProScan
  326. module name: InterProScan
    version 5.17-56.0
    Other versions: 5-RC7, 5.1-44.0, 5.10-50.0, 5.11-51.0, 5.12-52.0, 5.13-52.0, 5.14-53.0, 5.15-54.0, 5.16-55.0, 5.2-45.0, 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

    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

    https://github.com/ebi-pf-team/interproscan/wiki/Interproscan5_17_56_ReleaseNotes
    InterPro version 56.0 data (includes Panther 10.0 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 your own directory. See instructions at
    /group/bioinfo/apps/apps/interproscan-5.17-56.0/README.local

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

  327. IPknot
  328. 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

  329. iPlant iRODS iCommands
  330. 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

  331. Isaac Aligner
  332. 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

  333. Isaac Variant Caller
  334. 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

  335. Java
  336. module name: java
    version 1.7.0_79
    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, 1.8.0, 1.8.0_05, 1.8.0_11, 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, 6, 7, 8

    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

  337. Jellyfish
  338. module name: jellyfish
    version 2.2.4
    Other versions: 1.1.11, 1.1.3, 1.1.4, 2.1.1

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

    Depends on gcc

  339. jemalloc
  340. 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

  341. JIGSAW:
  342. 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

  343. jModelTest
  344. 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

  345. KAAS - KEGG Automatic Annotation Server
  346. 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

  347. khmer
  348. 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

  349. KmerGenie
  350. 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

  351. kSNP
  352. 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

  353. L_RNA_scaffolder
  354. 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

  355. LAPACK Linear Algebra PACKage and BLAS
  356. module name: lapack
    version 3.4.2

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

    Depends on gcc

  357. libgcrypt
  358. module name: libgcrypt
    version 1.5.3

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

    Depends on libgpg-error

  359. libxml2
  360. module name: libxml2
    version 2.9.1

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

    Depends on gcc

  361. libxslt
  362. 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

  363. Lucy
  364. module name: lucy
    version 1.20p

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

    Depends on gcc

  365. lz4
  366. 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

  367. MACS
  368. module name: macs
    version 2.1.0
    Other versions: 1.4.2a, 1.4.2b, 2.0.10, 2.0.10-2.7.2

    Model-based Analysis for ChIP-Seq
    https://github.com/taoliu/MACS/
    Info: /group/bioinfo/apps/apps/MACS-2.1.0/README.rst

    Depends on biopython/2.7.8
    Depends on PeakSplitter

  369. MAFFT
  370. 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

  371. MAKER
  372. module name: MAKER
    version 2.31.8-nompi
    Other versions: 2.10, 2.27b, 2.28b, 2.30p, 2.31.7, 2.31.8, 2.31.8-openmpi-1.6.5, 2.31.8-openmpi-1.8.1, 2.31.8-openmpi-1.8.8

    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-2.31.8-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

  373. MAQ
  374. 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

  375. MaSuRCA (Maryland Super Read Cabog Assembler)
  376. module name: MaSuRCA
    version 3.1.3-CentOS6
    Other versions: 2.1.0, 3.1.3

    Genome assembler
    http://www.genome.umd.edu/masurca.html
    Manual: http://www.genome.umd.edu/docs/MaSuRCA_QuickStartGuide.pdf
    Info: man jellyfish

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

    Depends on gcc

  377. MATLAB Compiler Runtime (MCR)
  378. 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

  379. matrix2png
  380. 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

  381. Mauve
  382. module name: mauve
    version 2.3.1

    http://asap.ahabs.wisc.edu/software/mauve/overview.html
    Construct multiple genome alignments in the presence of
    large-scale evolutionary events such as rearrangement and inversion
    Manual: http://gel.ahabs.wisc.edu/mauve/mauve-user-guide
    Manual: /group/bioinfo/apps/apps/mauve_2.3.1/mauve_user_guide.pdf
    Note: Needs X11 support for GUI (not needed with command line
    utilities mauveAligner or progressiveMauve)


    Depends on java

  383. mbuffer
  384. 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

  385. mcl
  386. module name: mcl
    version 12-068

    The Markov Cluster Algorithm (MCL)
    MCL algorithm finds cluster structure in graphs
    http://www.micans.org/mcl/index.html?sec_description1
    http://www.micans.org/mcl/index.html
    man pages available

    Depends on gcc

  387. MeDUSA
  388. 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

  389. MEGAN (MEtaGenome ANalyzer)
  390. module name: MEGAN
    version 5.2.3
    Other versions: 4.70.4, 5.1.4

    Software for analyzing metagenomes
    http://ab.inf.uni-tuebingen.de/software/megan5/
    Release Notes: http://ab.inf.uni-tuebingen.de/data/software/megan5/download/release_notes.txt
    Need X11 support for program to run (ssh -X)
    Need license key from http://www-ab2.informatik.uni-tuebingen.de/software/megan/register

    Depends on java

  391. MEME suite (Multiple Em for Motif Elicitation)
  392. 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

  393. MeQA
  394. 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

  395. MetaCV
  396. 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

  397. MetaVelvet
  398. 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

  399. methylQA
  400. 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

  401. METIS
  402. 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

  403. MFEprimer
  404. 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

  405. Microbiome Utilities Portal of the Broad Institute
  406. 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

  407. MicroRazerS
  408. 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

  409. Minia
  410. 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

  411. MIRA
  412. 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

  413. miRDeep
  414. module name: mirdeep
    version 2.0.0.7
    Other versions: 2.0.0.4

    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

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

  415. miRDeep-P
  416. 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

  417. MIREAP
  418. 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

  419. miRExpress
  420. module name: miRExpress
    version 2.1.3

    Analyzing high-throughput sequencing data for profiling microRNA expression
    http://mirexpress.mbc.nctu.edu.tw/
    Usage: /group/bioinfo/apps/apps/miRExpress-2.1.3/README
    Includes data from miRBase 18.0 (2012APR27)

    Depends on gcc

  421. miRNAkey
  422. 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

  423. MITObim
  424. module name: MITObim
    version 1.7
    Other versions: 1.6

    Mitochondrial baiting and iterative mapping
    https://github.com/chrishah/MITObim
    Version 1.7 uses mira 4.0.x
    Info: /group/bioinfo/apps/apps/MITObim-1.7/README.md
    Test data: /group/bioinfo/apps/apps/MITObim-1.7/testdata1.tgz

    Depends on perl
    Depends on mira

  425. Mono
  426. module name: mono
    version 4.0.2

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

    Depends on gcc

  427. MOTHUR
  428. module name: mothur
    version 1.34.4
    Other versions: 1.25.0, 1.25.1, 1.32.1

    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

  429. MrBayes
  430. module name: mrbayes
    version 3.2.5
    Other versions: 3.2.1

    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 openmpi/1.8.1_gcc-4.7.2

  431. MSPC (Multiple Sample Peak Calling)
  432. 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

  433. Mugsy
  434. module name: Mugsy
    version 1r2.3

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

    Depends on gcc
    Depends on muscle

  435. MUMmer
  436. 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

  437. MUSCLE
  438. 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

  439. MySQL Connector/J
  440. 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

  441. NCBI BLAST
  442. module name: blast
    version 2.3.0+
    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+

    Basic Local Alignment Search Tool
    http://blast.ncbi.nlm.nih.gov/
    http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
    http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
    Manuals: http://www.ncbi.nlm.nih.gov/books/NBK1762
    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

    Depends on gcc

  443. NCBI BLAST CGI programs
  444. 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

  445. NCBI Entrez Direct
  446. 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

  447. NCBI nseg
  448. 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

  449. ncoils
  450. 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

  451. NetBeans IDE
  452. 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

  453. NetBox
  454. 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

  455. Netpbm
  456. 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

  457. NextClip
  458. 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

  459. ngsplot
  460. module name: ngsplot
    version 2.47
    Other versions: 2.41.3

    Visualize next-generation sequencing (NGS) samples at functional genomic regions
    https://code.google.com/p/ngsplot/
    Example data: /group/bioinfo/apps/apps/ngsplot-2.47/example

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

  461. Novocraft
  462. 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

  463. NPS (Nucleosome Positioning from Sequencing)
  464. 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

  465. NSeq
  466. module name: NSeq
    version 1.0

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

    Depends on java

  467. Oases
  468. 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

  469. OpenMPI
  470. 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

  471. OrthoMCL DB
  472. 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

  473. PAGIT
  474. 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

  475. PAML (Phylogenetic Analysis by Maximum Likelihood)
  476. 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

  477. PANDAseq
  478. 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

  479. Parallel-meta
  480. 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

  481. ParsInsert
  482. 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

  483. PBSuite
  484. 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

  485. PCAP (Parallel Contig Assembly Program)
  486. 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

  487. PeakSplitter
  488. 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

  489. Perl
  490. 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
    Depends on ImageMagick/6.8.9-8
    Depends on expat

  491. Phobius
  492. module name: phobius
    version 1.01

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

    Depends on gcc

  493. Phobos
  494. 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

  495. phrap
  496. 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

  497. phred
  498. 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

  499. Phusion Assembler
  500. 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

  501. Phusion2
  502. 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

  503. PHYLIP (PHYLogeny Inference Package)
  504. 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

  505. PhyML
  506. 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

  507. Picard
  508. module name: picard-tools
    version 2.0.1
    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

    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

    Picard-tools JAR files are at /group/bioinfo/apps/apps/picard-tools-2.0.1
    Use "PicardCommandLine" command for summary
    Or, use "java [jvm-options] -jar $PICARD/picard.jar [options]" for more control

    Depends on java/8
    Depends on gcc

  509. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)
  510. 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

  511. Pindel
  512. module name: Pindel
    version 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
    http://gmt.genome.wustl.edu/packages/pindel/install.html

    This is Pindel version 0.2.5a7, Sept 16 2014.
    This program probably doesn't work

    Depends on gcc
    Depends on perl

  513. platanus
  514. 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

  515. PolyPhen-2 (Polymorphism Phenotyping v2)
  516. 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

  517. pplacer
  518. 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

  519. Primer3
  520. module name: primer3
    version 2.3.6
    Other versions: 1.1.4, 2.3.4

    Program for designing PCR primers
    http://primer3.sourceforge.net/
    Manual: /group/bioinfo/apps/apps/primer3-2.3.6/primer3_manual.htm

    Depends on gcc

  521. Prodigal l (Prokaryotic Dynamic Programming Genefinding Algorithm)
  522. module name: prodigal
    version 2.60

    Microbial (bacterial and archaeal) gene finding program
    https://code.google.com/p/prodigal/
    http://compbio.ornl.gov/prodigal/
    Info: /group/bioinfo/apps/apps/prodigal-2.60/README
    Forum: http://groups.google.com/group/prodigal-discuss

    Depends on gcc

  523. Program to Assemble Spliced Alignments (PASA)
  524. 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

  525. ProtTest
  526. 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

  527. Pscan_ChIP
  528. 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

  529. PyQt
  530. module name: PyQt
    version 4.9.4

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

    Depends on biopython

  531. pyRAD
  532. 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

  533. pysam
  534. 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

  535. Python with bioinformatics modules
  536. module name: biopython
    version 2.7.2
    Other versions: 2.7.3, 2.7.8

    http://python.org/
    Install info: http://docs.python.org/install/index.html

    Depends on python/2.7.2

  537. PyVCF
  538. 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

  539. QDD
  540. 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

  541. QIIME (Quantitative Insights Into Microbial Ecology)
  542. module name: Qiime
    version 1.9.1
    Other versions: 1.6.0, 1.7.0, 1.8.0, 1.9.0

    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/

    Depends on gcc
    Depends on tcl
    Depends on igraph
    Depends on R-bioconductor/3.1.2
    Depends on HDF5
    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

  543. QTL Cartographer
  544. 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

  545. Quake
  546. 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

  547. QualiMap
  548. module name: qualimap
    version 2.1.3
    Other versions: 0.6, 1.0, 2.1.1

    Graphical and command-line interface for quality control
    of alignment sequencing data
    http://qualimap.bioinfo.cipf.es/
    Manual: /group/bioinfo/apps/apps/qualimap_v2.1.3/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

  549. QUAST
  550. 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

  551. QuEST
  552. 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

  553. Quip
  554. 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

  555. R with Bioconductor libraries
  556. 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

    Statistics processing language with bioinformatics libraries
    http://www.r-project.org/
    http://www.bioconductor.org/

    Depends on gcc
    Depends on rhel5libs

  557. RADtools
  558. 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

  559. RandA
  560. 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

  561. Randfold
  562. 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

  563. RAPsearch (Reduced Alphabet based Protein similarity Search)
  564. module name: RAPsearch
    version 2.16
    Other versions: 2.12

    Fast protein similarity search
    http://omics.informatics.indiana.edu/mg/RAPSearch2/
    Info: /group/bioinfo/apps/apps/RAPsearch-2.16/readme

    Depends on gcc

  565. RAxML (standard edition)
  566. module name: RAxML
    version standard-5_7_2012

    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

  567. Ray
  568. 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 openmpi/1.8.1_gcc-4.7.2

  569. REAPR (Recognising Errors in Assemblies using Paired Reads)
  570. 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

  571. RECON
  572. 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

  573. RepARK
  574. 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

  575. RepeatMasker
  576. module name: RepeatMasker
    version 4.0.6
    Other versions: 3.3.0, 4.0.0, 4.0.1, 4.0.2, 4.0.3, 4.0.5

    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-4.0.6/repeatmasker.help
    FAQ: http://www.repeatmasker.org/faq.html

    DFAM Library Version = 2.0
    RepeatMasker & Repbase Library Version = 20150807

    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

  577. RepeatModeler
  578. module name: RepeatModeler
    version 1.0.8
    Other versions: 1.0.7

    De-novo repeat family identification and modeling package
    http://www.repeatmasker.org/RepeatModeler.html
    Manual: /group/bioinfo/apps/apps/RepeatModeler-1.0.8/README

    Depends on RepeatMasker
    Depends on RepeatScout
    Depends on RECON

  579. RepeatScout
  580. module name: RepeatScout
    version 1.0.5

    Identify repeat sequences from genomes without curated databases
    http://bix.ucsd.edu/repeatscout/
    Manual: http://bix.ucsd.edu/repeatscout/readme.1.0.5.txt
    Manual: /group/bioinfo/apps/apps/RepeatScout-1.0.5/README

    Depends on perl
    Depends on trf
    Depends on nseg

  581. rMATS
  582. 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

  583. RMBlast
  584. 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+

  585. RNA-SeQC
  586. 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

  587. RNAmmer
  588. module name: rnammer
    version 1.2

    Predicts ribosomal RNA genes in prokaryotic genome sequences
    http://www.cbs.dtu.dk/services/RNAmmer/
    Info: man rnammer

    Depends on HMMER/2.3.2

  589. Rockhopper
  590. 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

  591. ROOT
  592. 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

  593. RSEG
  594. 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

  595. RSEM
  596. module name: rsem
    version 1.2.25
    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, 1.2.7

    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/3.1.0
    Depends on perl
    Depends on bowtie
    Depends on bowtie2
    Depends on STAR

  597. RSeQC
  598. module name: RSeQC
    version 2.6.3

    Evaluate high throughput sequence data especially RNA-seq data
    http://rseqc.sourceforge.net/

    Depends on biopython/2.7.8
    Depends on R-bioconductor/3.1.2

  599. rtax
  600. 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

  601. Ruby
  602. 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

  603. samstat
  604. module name: samstat
    version 1.08

    Displaying sequence statistics for next generation sequencing
    http://samstat.sourceforge.net/

    Depends on gcc

  605. SAMtools
  606. module name: samtools
    version 1.3
    Other versions: 0.1.16, 0.1.18, 0.1.19, 0.2.0-devel-29-July-2014, 1.0, 1.1, 1.2

    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/1.3
    Depends on bcftools/1.3

  607. SCaFoS (Selection, Concatenation and Fusion of Sequences)
  608. 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

  609. SeqAlto
  610. 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

  611. seqbuster
  612. 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

  613. SeqPrep
  614. 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

  615. seqtk
  616. 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

  617. Sequence Cleaner
  618. 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

  619. SequenceServer
  620. 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

  621. SeqyClean
  622. 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

  623. SGA String Graph Assembler
  624. 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

  625. ShellCheck
  626. module name: shellcheck
    version 0.3.8

    A shell script static analysis tool
    https://github.com/koalaman/shellcheck

    Depends on haskell-platform

  627. SHORE (Short Read)
  628. 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

  629. SHOREmap
  630. module name: SHOREmap
    version 3.0

    Fast and accurate identification of causal mutations in plants
    http://bioinfo.mpipz.mpg.de/shoremap/index.html

    Depends on DISLIN
    Depends on SHORE

  631. SHRiMP
  632. 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

  633. SICER
  634. 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

  635. SignalP
  636. 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

  637. SiLiX
  638. 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

  639. SMRT Analysis
  640. 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!

  641. SNAP
  642. 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

  643. SNAP (Semi-HMM-based Nucleic Acid Parser)
  644. 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

  645. snpEff and snpSift
  646. module name: snpEff
    version 4.1d
    Other versions: 3.3F, 3.6, 4.0e, 4.1

    Genetic variant annotation and effect prediction toolbox
    http://snpeff.sourceforge.net/index.html
    Manual: http://snpeff.sourceforge.net/SnpEff_manual.html
    Need X11 display?
    Need databases
    Probably need to indicate JAR file location:
    java -jar $snpEff_root/snpEff.jar ...

    Depends on java

  647. SNPhylo
  648. 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

  649. SOAPaligner
  650. 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

  651. SOAPdenovo
  652. 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

  653. SOAPdenovo-Trans
  654. 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

  655. SOAPfuse
  656. 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

  657. SOAPfusion
  658. 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

  659. SOAPsplice
  660. 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

  661. SOAPsv
  662. 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

  663. SolexaQA
  664. 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

  665. Some RHEL 5 shared libaries
  666. 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

  667. SourceTracker
  668. 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/

  669. SPAdes
  670. module name: spades
    version 3.7.0
    Other versions: 2.2.1, 2.3.0, 3.0.0, 3.1.0, 3.1.1, 3.5.0, 3.5.0-p1, 3.5.0-p2, 3.6.0, 3.6.1, 3.6.2

    Genome assembler for multicell and single-cell MDA bacteria
    http://bioinf.spbau.ru/spades
    Manual: http://spades.bioinf.spbau.ru/release3.6.2/manual.html
    Manual: /group/bioinfo/apps/apps/spades-3.7.0/share/spades/manual.html


    Depends on gcc
    Depends on biopython/2.7.8

  671. sparsehash
  672. 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

  673. SplAdder
  674. 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

  675. SpliceGrapher
  676. 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

  677. SQUID
  678. module name: squid
    version 1.9g

    C function library for sequence analysis
    http://selab.janelia.org/software.html (search for "SQUID")
    Documentation on web site and man pages

    Depends on gcc

  679. SRA Toolkit
  680. module name: sra-toolkit
    version 2.5.7
    Other versions: 2.1.6, 2.3.5, 2.4.2, 2.5.1, 2.5.2

    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-2.5.7/help

    Includes taxid2wgs.pl for WGS data searches
    Ref: https://github.com/ncbi/sra-tools/wiki/HowTo:-Binary-Installation

    Hint: use $SRATOOLKIT/sra-command to run a command
    For example: $SRATOOLKIT/fastq-dump --stdout -X 2 SRR390728
    Also might need to configure with "$SRATOOLKIT/vdb-config -i"

    Depends on perl

  681. SSPACE
  682. 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/
    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

  683. SSPACE-LongRead
  684. module name: SSPACE-LongRead
    version 1-1

    Scaffolding pre-assembled contigs using long reads
    http://www.baseclear.com/lab-products/bioinformatics-tools/sspace-longread/

  685. Stacks
  686. 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

  687. Stampy
  688. 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

  689. Stanford Network Analysis Platform (SNAP)
  690. 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

  691. STAR
  692. module name: STAR
    version 2.5.1b
    Other versions: 2.4.0j, 2.4.0k, 2.4.1d, 2.4.2a, 2.5.0c

    RNA-seq aligner
    https://github.com/alexdobin/STAR
    Manual: /group/bioinfo/apps/apps/STAR-2.5.1b/doc/STARmanual.pdf
    Info: /group/bioinfo/apps/apps/STAR-2.5.1b/README.md
    Info: /group/bioinfo/apps/apps/STAR-2.5.1b/RELEASEnotes.md
    Info: /group/bioinfo/apps/apps/STAR-2.5.1b/CHANGES.md

    Depends on gcc

  693. storm
  694. 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

  695. StringTie
  696. module name: stringtie
    version 1.0.2
    Other versions: 1.0.1

    Transcript assembly and quantification for RNA-Seq
    http://ccb.jhu.edu/software/stringtie/
    Info: /group/bioinfo/apps/apps/stringtie-1.0.2/README

    Depends on gcc

  697. Structure
  698. 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

  699. SUMATRA and SUMACLUST
  700. 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

  701. SWIG
  702. 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

  703. T-COFFEE
  704. 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

  705. T-lex
  706. 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

  707. tabix
  708. 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

  709. Target Finder
  710. 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

  711. TASR pipeline
  712. 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

  713. TASSEL
  714. module name: TASSEL
    version 5.2.9

    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

  715. tbl2asn
  716. module name: tbl2asn
    version 22.9

    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-22.9/tbl2asn.txt

    Depends on gcc

  717. Tcl/Tk (Tool Command Language)
  718. 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

  719. TeX Live
  720. module name: texlive
    version 2013

    TeX document production system
    http://www.tug.org/texlive/

    Depends on gcc

  721. tidyp
  722. module name: tidyp
    version 1.04

    Validate HTML
    http://tidyp.com/

    Depends on gcc

  723. TMHMM
  724. 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

  725. TopHat
  726. module name: tophat
    version 2.1.0
    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

    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

    Depends on gcc
    Depends on zlib
    Depends on bowtie2
    Depends on bowtie
    Depends on blast
    Depends on biopython/2.7.8

  727. trans-ABySS
  728. module name: trans-abyss
    version 1.5.1
    Other versions: 1.3.2

    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-1.5.1/TUTORIAL.txt
    Support: http://groups.google.com/group/trans-abyss

    Depends on abyss
    Depends on biopython/2.7.8
    Depends on blat
    Depends on bowtie2
    Depends on gmap
    Depends on samtools/1.0

  729. TransDecoder
  730. module name: TransDecoder
    version 2.0.1

    Find Coding Regions Within Transcripts
    http://transdecoder.github.io/

    Depends on perl

  731. Transrate
  732. 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

  733. Tree Puzzle
  734. 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

  735. TRF (Tandem Repeats Finder)
  736. module name: trf
    version 4.04

    Locate and display tandem repeats in DNA sequences
    http://tandem.bu.edu/trf/trf.html

  737. TrimAl
  738. module name: trimal
    version 1.2r59

    Removes spurious or poorly aligned regions from a multiple sequence alignment
    http://trimal.cgenomics.org/

    Depends on gcc

  739. Trimmomatic
  740. module name: trimmomatic
    version 0.32
    Other versions: 0.17, 0.20, 0.22, 0.30

    A flexible read trimming tool for Illumina NGS data
    http://www.usadellab.org/cms/index.php?page=trimmomatic
    Use "trimmomatic" to start the program

    Depends on java

  741. Trinity
  742. module name: trinity
    version 2.1.1
    Other versions: 2.0.2, 2.0.3, 2.0.6, 2.1.0, 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, r20131110, r2013_08_14, 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-2.1.1/Release.Notes

    For parallel processing with PBS support; see:
    /group/bioinfo/apps/apps/trinityrnaseq-2.1.1/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 bowtie
    Depends on bowtie2
    Depends on R-bioconductor/3.1.0
    Depends on PASA
    Depends on express

  743. Trinity (development version)
  744. 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

  745. Trinotate
  746. module name: trinotate
    version 2.0.2
    Other versions: r20131110

    Transcriptome functional annotation and analysis
    http://trinotate.github.io/

    Prebuilt SQLite database with Unitprot (swissprot & uniref90) annotation information
    at /group/bioinfo/apps/apps/Trinotate-2.0.2/data/Trinotate.sqlite

    Copy that database to a directory owned by you and use it from there.


    Depends on trinity
    Depends on blast
    Depends on signalp
    Depends on tmhmm
    Depends on rnammer

  747. tRNAscan-SE
  748. 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

  749. uclust
  750. 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

  751. UNAFold
  752. 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

  753. usearch
  754. module name: usearch
    version 5.2.236
    Other versions: 6.1.544, 7, 7.0.1090, 7.0.959, 8, 8.0.1517, 8.0.1623

    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


  755. USeq
  756. 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

  757. util-linux
  758. 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

  759. vcflib
  760. 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

  761. VCFtools
  762. 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

  763. Velvet
  764. 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

  765. VelvetOptimizer
  766. 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

  767. ViennaRNA
  768. module name: ViennaRNA
    version 2.1.1
    Other versions: 1.8.5, 2.0.7, 2.2.4

    RNA Secondary Structure Prediction and Comparison
    http://www.tbi.univie.ac.at/~ronny/RNA/
    Manual: /group/bioinfo/apps/apps/ViennaRNA-2.1.1/share/doc/ViennaRNA/RNAlib-2.1.1.pdf
    Documentation on web site and man pages

  769. Vmatch
  770. module name: Vmatch
    version 2.2.4

    Large scale sequencer analysis software
    http://www.vmatch.de/
    Manual: /group/bioinfo/apps/apps/vmatch-2.2.4/virtman.pdf
    Manual: http://www.vmatch.de/virtman.pdf

    Depends on gcc
    Depends on perl

  771. vsearch
  772. module name: vsearch
    version 1.4.7

    Metagenomics tool; free replacement for usearch
    https://github.com/torognes/vsearch
    Manual: /group/bioinfo/apps/apps/vsearch-1.4.7/doc/vsearch_manual.pdf
    or use "man vsearch"


  773. WebLogo
  774. 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

  775. WIGGLER (a.k.a. align2rawsignal)
  776. 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

  777. XZ Utils
  778. module name: xz
    version 5.0.5

    Free general-purpose data compression software with high compression ratio
    http://tukaani.org/xz/
    Info: /group/bioinfo/apps/apps/xz-5.0.5/share/doc/xz/
    man pages available


    Depends on gcc

  779. zlib
  780. module name: zlib
    version 1.2.8
    Other versions: 1.2.7

    Free compression library
    http://www.zlib.net/
    man -s3 zlib

    Depends on gcc
Updated: Thu Mar 31 12:39:26 2016
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