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CVMFS Modules

Bioinformatics resources

C3G, in partnership with Compute Canada, offers and maintains a large set of bioinformatics resources for the community. Below is a list of software currently deployed on several HPC centres, including Guillimin, Cedar, Graham and Mammouth. Several reference genomes are also available.

To access these modules, you need to add the following lines to your .bashrc file.

Copy to Clipboard

To explore the available tools, you can type:

Copy to Clipboard

To load a module, for example samtools, you can use:

Copy to Clipboard

Available Modules


3DChromatin_ReplicateQC | ABySS | Accurity | AMOS | Anaconda | ARTIC | ASCAT | autoconf | bamtools | BBMap | bcbio.variation | bcbio.variation.recall | bcftools | beagle | bedops | bedtools | bio-playground | bismark | BisSNP | blast | Boost C++ Libraries | bowtie | bowtie2 | breakdancer | breakseq2 | butter | bwa | bwakit | Canu | cd-hit | Cell Ranger | Cell Ranger ARC | Cell Ranger ATAC | Cl Range DNA | CHiCAGO | ChromImpute | circos | circos-tools | CNVkit | COBALT | CoVSeQ Tools | CrossMap | cufflinks | cutadapt | deepTools | Delly | demuxlet | DUK | duphold | ea-utils | emboss | EPACTS | exonerate | ExpansionHunterDenovo | export2graphlan | fastp | fastqc | FastTree | FASTX | fgbio | FLASH | freebayes | FusionCatcher | GangSTR | gcta | gemBS | gemini | GEM library | GenomeTools | GenPipes | ghostscript | GraPhlAn | gsort | gsutil | Hclust2 | HCP tools | HDF5 | hicup | HiCUP | hmmer | homer | htslib | idba | igv | igvtools | ImageMagick | ivar | Jellyfish | Juicer | kaiju | kallisto | kmergenie | kraken2 | KronaTools | LAST | libStatGen | LUMPY-SV | MACS2 | mafft | Manta | Medaka | MELT | metawrap | minimap2 | mirdeep2 | mosdepth | MUGQIC pipelines | MUGQIC TOOLS | MultiQC | MUMmer | MUSCLE | Nanopolish | ncov-tools | NextClip | Octopus | pandoc | GNU parallel | PBSuite | Perl | picard | pigz | prodigal | Prokka | PURPLE | qualimap | Quast | R_Bioconductor | RAPSearch2 | ray | RepeatMasker | RNAmmer | RNA-SeQC | rsem | Ruby | Salmon | sambamba | samblaster | samtools | scalpel | SCoNEs | Seq2Fun | SeqKit | seqtk | Sequenza-utils | ShortStack | SignalP | simple_sv_annotation | skewer | Smoove | SMRT Analysis | SMRTLink | snap | snpEff | SPAdes | SparseHash | Sphinx | SplAdder | SRA Toolkit | Stacks | star | STAR-Fusion | Strelka2 | StringTie | Supernova | SURPI | SvABA | SVTyper | tabix | TelSeq | TMHMM | tophat | TransDecoder | TRF | trimmomatic | trinity | trinotate | UCSC User Apps | USEARCH | VarDictJava | variantbam | VarScan | vawk | vcf2db | vcfanno | vcflib | vcftools | velvet | verifyBamID | vg | ViennaRNA | VIP | vsearch | vt | weblogo | wgs-assembler | WHAM | wub | zlib |

List of Modules

3DChromatin_ReplicateQC
Software to compute reproducibility and quality scores for Hi-C data

Versions Available: (1.0.1

ABySS
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Versions Available: (2.0.2,1.3.5

Accurity
Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome may work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).

Versions Available: (32acfd1e-debug

AMOS
A Modular, Open-Source whole genome assembler

Versions Available: (3.1.0

Anaconda
Anaconda is a free and open-source distribution of the programming languages Python and R. The distribution comes with the Python interpreter and various packages related to machine learning and data science.

Versions Available: (2-4.0.0

ARTIC
iThe ARTIC field bioinformatics pipeline for working with virus sequencing data sequenced with nanopore

Versions Available: (1.2.1

ASCAT
ASCAT is a method to derive copy number profiles of tumour cells,,accounting for normal cell admixture and tumour aneuploidy (Figure 1).,ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the,amount of DNA per tumour cell, expressed as multiples of haploid genomes),from SNP array or massively parallel sequencing data, and calculates,whole-genome allele-specific copy number profiles (the number of copies of,both parental alleles for all SNP loci across the genome).

Versions Available: (2.3

autoconf
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.

Versions Available: (2.69

bamtools
C++ API & command-line toolkit for working with BAM data

Versions Available: (2.5.1,2.4.1

BBMap
BBMap is a short read aligner, as well as various other bioinformatic tools.

Versions Available: (38.90

bcbio.variation
Toolkit to analyze genomic variation data, built on the GATK with Clojure

Versions Available: (0.2.6

bcbio.variation.recall
Parallel merging, squaring off and ensemble calling for genomic variants

Versions Available: (0.2.6,0.1.7

bcftools
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

Versions Available: (1.15,1.14,1.12,...

beagle
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.

Versions Available: (03May16.862,r1399

bedops
High-performance genomic feature operations.

Versions Available: (v2.4.35,v2.4.28

bedtools
A powerful toolset for genome arithmetic

Versions Available: (2.29.2,2.27.0,2.26.0,...

bio-playground
Miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

Versions Available: (master

bismark
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.

Versions Available: (0.21.0,0.18.2,0.18.1,...

BisSNP
A bisulfite space genotyper & methylation caller

Versions Available: (0.82.2

blast
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

Versions Available: (2.10.0+,2.9.0+,2.7.1+,...

Boost C++ Libraries
Boost provides free peer-reviewed portable C++ source libraries.

Versions Available: (1.66.0,1.63.0

bowtie
An ultrafast memory-efficient short read aligner

Versions Available: (1.3.1,1.2.2,1.2.0,...

bowtie2
Fast and sensitive gapped read alignment

Versions Available: (2.3.5,2.3.1,2.3.0,...

breakdancer
SV detection from paired end reads mapping

Versions Available: (1.1_2011_02_21

breakseq2
BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.

Versions Available: (2.2

butter
butter: Bowtie UTilizing iTerative placEment of Repetitive small rnas

Versions Available: (0.3.3

bwa
The BWA read mapper.

Versions Available: (0.7.17,0.7.15,0.7.12,...

bwakit
A self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping

Versions Available: (0.7.15,0.7.12

Canu
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.

Versions Available: (1.5

cd-hit
Clusters and compares protein or nucleotide sequences

Versions Available: (4.5.4-2011-03-07

Cell Ranger
Cell Ranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

Versions Available: (7.0.1,6.1.1,6.0.2,...

Cell Ranger ARC
Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.

Versions Available: (2.0.0,1.0.1

Cell Ranger ATAC
Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.

Versions Available: (2.0.0,1.1.0,1.0.1,...

Cl Range DNA
Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.

Versions Available: (1.0.0

CHiCAGO
CHiCAGO is a set of tools for calling significant interactions in Capture HiC data, such as Promoter Capture HiC.

Versions Available: (1.19.0,1.1.5

ChromImpute
ChromImpute is software for large-scale systematic epigenome imputation.

Versions Available: (1.0.3

circos
Circos is a software package for visualizing data and information. It visualizes data in a circular layout

Versions Available: (0.69-6

circos-tools
circos-tools provides several utility add-on scripts, such as for bundling links

Versions Available: (0.23

CNVkit
Copy number variant detection from high-throughput sequencing

Versions Available: (0.9.5

COBALT
Determines the read depth ratios of the supplied tumor and reference genomes.

Versions Available: (1.13,1.11

CoVSeQ Tools
A collection of tools and scripts to support the analysis and collect metrics on COVID-19 viral data.

Versions Available: (1.2.1,1.2.0,1.1.1,...

CrossMap
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies.

Versions Available: (0.5.2

cufflinks
Transcriptome assembly and differential expression analysis for RNA-Seq.

Versions Available: (2.2.1

cutadapt
Trim adapters from high-throughput sequencing reads

Versions Available: (2.10,2.9

deepTools
A set of user-friendly tools for normalization and visualzation of deep-sequencing data

Versions Available: (3.5.1,3.5.0,3.3.1,...

Delly
Structural variant discovery by integrated paired-end and split-read analysis

Versions Available: (0.8.1,0.7.9,0.7.8,...

demuxlet
Genetic multiplexing of barcoded single cell RNA-seq

Versions Available: (master_20210203,master_20210204,master_20190913

DUK
Duk is a fast, accurate,and memory efficent DNA sequence matching tool.

Versions Available: (1.1

duphold
SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls.

Versions Available: (0.1.1

ea-utils
Command-line tools for processing biological sequencing data.

Versions Available: (1.1.2-537

emboss
The European Molecular Biology Open Software Suite

Versions Available: (6.6.0,6.4.0

EPACTS
Efficient and Parallelizable Association Container Toolbox. Perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface.

Versions Available: (3.2.6

exonerate
Exonerate - A generic tool for pairwise sequence comparison / alignment

Versions Available: (2.2.0

ExpansionHunterDenovo
ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).

Versions Available: (0.8.7

export2graphlan
Conversion software tool for producing both annotation and tree files for GraPhlAn.

Versions Available: (0.22

fastp
A FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting…)

Versions Available: (0.23.2,0.19.7

fastqc
A quality control tool for high throughput sequence data.

Versions Available: (0.11.6.devel,0.11.5,0.11.2

FastTree
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences

Versions Available: (2.1.10,2.1.7

FASTX
FASTA/FASTQ pre-processing programs

Versions Available: (0.0.14

fgbio
A set of tools for working with genomic and high throughput sequencing data, including UMIs

Versions Available: (1.4.0,1.3.0,1.1.0,...

FLASH
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

Versions Available: (1.2.11,1.2.8

freebayes
Bayesian haplotype-based polymorphism discovery and genotyping

Versions Available: (1.3.4,1.2.0

FusionCatcher
Finder of Somatic Fusion Genes in RNA-seq data.

Versions Available: (0.99.7b

GangSTR
GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

Versions Available: (2.4.4

gcta
GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits.

Versions Available: (1.92.4beta

gemBS
gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

Versions Available: (3.3.0

gemini
a lightweight db framework for disease and population genetics.

Versions Available: (0.30.2,0.20.1,0.19.1,...

GEM library
A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper

Versions Available: (v1.315

GenomeTools
GenomeTools: Scripts and Classes For Working With Genomic Data.

Versions Available: (1.5.9

GenPipes
GenPipes is sponsored by Canadian Center for Computational Genomics (C3G). C3G has created a distributed innovation node with broad expertise in bioinformatics. It offers bioinformatics analysis and HPC services for the life sciences research community. These services include customized and case-by-case analysis, along with an extensive suite of software solutions for the genomics community.

Versions Available: (4.3.0,4.2.1,4.2.0,...

ghostscript
Ghostscript is an interpreter for the PostScript® language and PDF files

Versions Available: (8.70

GraPhlAn
GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.

Versions Available: (1.1.3

gsort
sort genomic files according to a genomefile

Versions Available: (0.1.4,0.0.6

gsutil
A command line tool for interacting with cloud storage services.

Versions Available: (4.61

Hclust2
Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.

Versions Available: (1.0.0

HCP tools
High speed file transfer

Versions Available: (1.2.5R_11

HDF5
High-performance data management and storage suite

Versions Available: (1.8.20

hicup
A tool for mapping and performing quality control on Hi-C data

Versions Available: (v0.7.2,v0.7.0,v0.5.9,...

HiCUP
A tool for mapping and performing quality control on Hi-C data

Versions Available: (v0.7.2,v0.7.0,v0.5.9,...

hmmer
Biosequence analysis using profile hidden Markov models

Versions Available: (3.1b1,3.1b2,2.3.2

homer
Software for motif discovery and next generation sequencing analysis

Versions Available: (4.11,4.9.1,4.7

htslib
C library for high-throughput sequencing data formats.

Versions Available: (1.14,1.12,1.11,...

idba
IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinformatics.

Versions Available: (1.1.3g1

igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics,data and annotations.

Versions Available: (2.3.23

igvtools
command line tools for IGV

Versions Available: (2.3.67,2.3.14

ImageMagick
Use ImageMagick® to create, edit, compose, or convert digital images.

Versions Available: (7.1.0-4

ivar
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Versions Available: (1.3,1.2.3,1.2.2,...

Jellyfish
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Versions Available: (2.3.0,2.2.6,2.1.3

Juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Versions Available: (1.11.09,0.7.0

kaiju
Fast and sensitive taxonomic classification for metagenomics

Versions Available: (1.7.3

kallisto
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Versions Available: (0.44.0

kmergenie
KmerGenie estimates the best k-mer length for genome de novo assembly

Versions Available: (1.5692

kraken2
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Versions Available: (2.1.0,2.0.9-beta

KronaTools
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

Versions Available: (2.6.1

LAST
LAST finds & aligns related regions of sequences.

Versions Available: (959

libStatGen
Useful set of classes for creating statistical genetic programs.

Versions Available: (1.0.13

LUMPY-SV
a general probabilistic framework for structural variant discovery

Versions Available: (0.2.13,master_20190208

MACS2
Model Based Analysis for ChIP-Seq data

Versions Available: (2.2.7.1,2.1.1.20160309,2.1.0.20151222,...

mafft
Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform

Versions Available: (7.310

Manta
Structural variant and indel caller for mapped sequencing data

Versions Available: (1.5.0

Medaka
Neural network sequence error correction.

Versions Available: (1.0.3

MELT
A nucleotide melt temp calculator

Versions Available: (2.1.5,2.1.4

metawrap
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Versions Available: (1.3

minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences.

Versions Available: (2.17

mirdeep2
A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs

Versions Available: (0.0.8,0.0.5

mosdepth
Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.

Versions Available: (0.2.4

MUGQIC pipelines
Former name of GenPipes :

Versions Available: (2.3.0,2.2.1,2.2.0,...

MUGQIC TOOLS
Miscenlenous tools developped in bash, perl, python or R at the BIinformatics plateform of the McGill University Genome Quebec Inovation Center

Versions Available: (2.10.10,2.10.9,2.10.8,...

MultiQC
Create aggregate bioinformatics analysis reports across many samples and tools

Versions Available: (v1.6,1.12,1.10.1,...

MUMmer
MUMmer is a system for rapidly aligning entire genomes

Versions Available: (3.23

MUSCLE
MUSCLE: multiple sequence alignment with high accuracy and high throughput

Versions Available: (3.8.31

Nanopolish
Signal-level algorithms for MinION data.

Versions Available: (0.13.3,0.11.1

ncov-tools
Small collection of tools for performing quality control on coronavirus sequencing data and genomes

Versions Available: (20200820,1.8,1.6

NextClip
Nextera Long Mate Pair analysis and processing tool

Versions Available: (b833dd9

Octopus
Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework.

Versions Available: (0.6.2-beta

pandoc
Universal markup converter

Versions Available: (2.16.2,1.15.2,1.13.1

GNU parallel
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.

Versions Available: (20210922,20170322,20130822

PBSuite
Software for Long-Read Sequencing Data from PacBio

Versions Available: (15.2.20beta

Perl
Perl is a family of two high-level, general-purpose, interpreted, dynamic programming languages.

Versions Available: (5.34.0,5.22.1,5.18.2

picard
Java tools for working with NGS data in the BAM format

Versions Available: (2.27.4,2.26.6,2.23.3,...

pigz
A parallel implementation of gzip for modern multi-processor, multi-core machines

Versions Available: (2.4,2.3

prodigal
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program

Versions Available: (2.6.3

Prokka
Rapid annotation of prokaryotic genomes

Versions Available: (1.12

PURPLE
PURPLE is a purity ploidy estimator for whole genome sequenced (WGS) data.

Versions Available: (3.4.1,2.53

qualimap
Quality control of alignment sequencing data and its derivatives like feature counts

Versions Available: (2.2.1,2.2.2dev

Quast
Quality Assessment Tool for Genome Assemblies

Versions Available: (5.0.2

R_Bioconductor
R is a language and environment for statistical computing and graphics. Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data and using the R statistical programming language, and is open source and open development.

Versions Available: (4.2.1_3.15,4.1.0_3.13,4.0.3_3.12,...

RAPSearch2
Tool for fast protein similarity searches (Reduced Alphabet based Protein similarity Search)

Versions Available: (2.24,2.12

ray
Parallel genome assemblies for parallel DNA sequencing

Versions Available: (2.3.1

RepeatMasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

Versions Available: (4.0.7

RNAmmer
Prediction of ribosomal RNA sub units

Versions Available: (1.2

RNA-SeQC
RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data.

Versions Available: (2.4.2,1.1.8,1.1.7

rsem
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Versions Available: (1.3.3,1.3.1,1.2.12

Ruby
A dynamic, open source programming language with a focus on simplicity and productivity.

Versions Available: (2.5.3

Salmon
Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Versions Available: (1.5.1,1.3.0

sambamba
Tools for working with SAM/BAM data

Versions Available: (0.8.2,0.8.1,0.8.0,...

samblaster
Mark duplicates in and extract discordant and split reads from SAM files.

Versions Available: (0.1.24

samtools
Tools for dealing with SAM, BAM and CRAM files

Versions Available: (1.14,1.12,1.11,...

scalpel
Sensitive detection of INDELs (INsertions and DELetions)

Versions Available: (0.5.2,0.3.2

SCoNEs
SCoNEs is a R script that allows estimating the Copy Number Variations in whole genome Next Generation Sequencing data.

Versions Available: (2.1.2,2.1.1

Seq2Fun
Seq2Fun is an ultrafast, all-in-one functional profiling tool for RNA-seq data analysis for organisms without reference genomes.

Versions Available: (1.2.5,1.2.2

SeqKit
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Versions Available: (0.11.0

seqtk
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format

Versions Available: (1.2,1.0,1.0-r82b

Sequenza-utils
Analysis of cancer sequencing samples, utilities for the R package sequenza

Versions Available: (3.0.0

ShortStack
ShortStack: Comprehensive annotation and quantification of small RNA genes

Versions Available: (3.3

SignalP
Prediction of the presence and location of signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences.

Versions Available: (4.1

simple_sv_annotation
Simplify snpEff annotations for interesting cases

Versions Available: (1.0.0

skewer
A fast and accurate adapter trimmer for paired-end reads.

Versions Available: (0.2.2

Smoove
structural variant calling and genotyping with existing tools, but, smoothly

Versions Available: (0.2.3,0.2.2

SMRT Analysis
Suite of analytical applications developed and optimized to anaylyse PacBio long-read sequencing data.

Versions Available: (2.3.0.140936.p4,2.3.0.140936.p2,2.3.0.140936.p5,...

SMRTLink
PACBIO SMRT Link is the web-based end-to-end workflow manager for the Sequel® Systems.

Versions Available: (11.0.0,10.1.0,9.0.0,...

snap
Semi-HMM-based Nucleic Acid Parser -- gene prediction tool

Versions Available: (1.0beta.18,0.15,2013-11-29

snpEff
Genetic variant annotation and effect prediction toolbox

Versions Available: (5.1,4.3,4.2,...

SPAdes
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

Versions Available: (3.13.0,3.10.0,3.7.1

SparseHash
Several hash-map implementations (C++ associative containers)

Versions Available: (2.0.3

Sphinx
Sphinx is a tool that makes it easy to create intelligent and beautiful documentation for Python projects.

Versions Available: (master

SplAdder
Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

Versions Available: (1.0.0

SRA Toolkit
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Versions Available: (2.10.5,2.8.2-1,2.6.2

Stacks
Stacks is a software pipeline for building loci from RAD-seq

Versions Available: (2.55,1.46

star
An RNA-seq read aligner.

Versions Available: (2.7.8a,2.7.2b,2.7.3a,...

STAR-Fusion
STAR-Fusion fusion variant caller. All dependencies required to run FusionInspector and FusionAnnotator are included.

Versions Available: (1.10.1,1.10.0,1.8.1

Strelka2
Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

Versions Available: (2.9.10

StringTie
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Versions Available: (2.1.4,1.3.5

Supernova
Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.

Versions Available: (2.1.1,2.0.1,1.2.2,...

SURPI
SURPI (Sequence-Based Ultra-Rapid Pathogen Identification) is a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data.

Versions Available: (1.0.18

SvABA
Structural variation and indel detection by local assembly

Versions Available: (1.1.0,0.2.1,0.2.2-beta

SVTyper
Bayesian genotyper for structural variants

Versions Available: (0.7.0

tabix
C library and command line tools for high-throughput sequencing data formats.

Versions Available: (0.2.6

TelSeq
A software for calculating telomere length

Versions Available: (0.0.2

TMHMM
Program for prediction of transmembrane helices in proteins

Versions Available: (2.0c

tophat
A spliced read mapper for RNA-Seq

Versions Available: (2.1.1,2.0.14,2.0.13

TransDecoder
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

Versions Available: (2.0.1

TRF
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.

Versions Available: (4.09

trimmomatic
A flexible read trimming tool for Illumina NGS data

Versions Available: (0.39,0.36,0.35,...

trinity
Trinity assembles transcript sequences from Illumina RNA-Seq data.

Versions Available: (2.8.6,2.2.0,2.2.0_patch,...

trinotate
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms

Versions Available: (20131110,2.0.2,2.0.1

UCSC User Apps
UCSC utilities (LiftOver, Blat, etc..) installed as standalone command-line tools

Versions Available: (20140212,v359,v346,...

USEARCH
Sequence analysis tool with high-throughput search and clustering algorithms.

Versions Available: (10.0.240,8.1.1861,5.2.236

VarDictJava
VarDictJava is a variant discovery program written in Java and Perl. It is a Java port of VarDict variant caller.

Versions Available: (1.4.10,1.4.9,1.4.8

variantbam
Filtering and profiling of next-generational sequencing data using region-specific rules

Versions Available: (1.4.3

VarScan
Variant calling and somatic mutation/CNV detection for next-generation sequencing data

Versions Available: (2.4.4,2.4.3,2.4.2,...

vawk
An awk-like VCF parser

Versions Available: (0.0.2

vcf2db
Create a gemini-compatible database from a VCF

Versions Available: (master_20180427,master.c391574_20210730

vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files

Versions Available: (0.3.3,0.3.2,0.2.9

vcflib
Command-line tools for manipulating VCF files

Versions Available: (1.0.1,1.0.0

vcftools
A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries

Versions Available: (0.1.14,0.1.11

velvet
Sequence Assembler for short reads

Versions Available: (1.2.10

verifyBamID
verifyBamID verifies identity and purity of sequence data

Versions Available: (1.1.3,devMaster_20151216

vg
Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods

Versions Available: (1.28.0

ViennaRNA
Vienna RNA package -- RNA secondary structure prediction and comparison

Versions Available: (2.4.14,2.3.3

VIP
Virus Identification Pipeline (VIP) was developed for metagenomic identification of viral pathogen.

Versions Available: (1.0.1

vsearch
a versatile open source tool for metagenomics (USEARCH alternative)

Versions Available: (1.11.1

vt
A tool set for manipulating and generating VCF files

Versions Available: (0.57

weblogo
WebLogo3 : Sequence Logos Redrawn

Versions Available: (3.5.0,3.3,2.8.2

wgs-assembler
Celera Assembler (wgs-assembler) is a de novo whole-genome shotgun (WGS) DNA sequence assembler

Versions Available: (8.1

WHAM
Structural variant detection and association testing

Versions Available: (1.8.0

wub
Tools and software library developed by the ONT Applications group

Versions Available: (0.5.1

zlib
A Massively Spiffy Yet Delicately Unobtrusive Compression Library (Not Related to the Linux zlibc Compressing File-I/O Library)

Versions Available: (1.2.11