Name	Description	Versions	Origin
_genome2-legacy	many tools will not work on the Slurm cluster because it may lack a lot of system library. many tools will not work on the Slurm cluster because it may lack a lot of system library.	NA, NA
abyss	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	2.2.1
adxv	adxv can be used to display and analyze 2-D area detector data. It is optimized to display X-Ray crystallography diffraction images.	1.9.14
alientrimmer	Trimmer of contaminant oligonucleotide sequences such as primers and adapters	0.4.1
anvio	An interactive analysis and visualization platform for omics data	6.1, 4.0.0, 5.2.0, 5.5.0, 6.0.0
arcs	Scaffolding genome sequence assemblies using 10X Genomics data	1.1.0
assemblytics	analyze a genome assembly by comparing it to a reference genome	1.2.1
augustus	AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.	3.3.3, 3.3.2
bam2fastx	Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files	1.3.0
bc	bc is an arbitrary precision numeric processing language.	1.07.1
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.	1.9, 1.10.2, 1.6
bcl2fastq	The Illumina bcl2fastq2 Conversion Software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.	2.20.0
bedtools	A powerful toolset for genome arithmetic	2.26.0, 2.27.1, 2.29.2
berokka	Trim, circularise and orient long read bacterial genome assemblies.	0.2.3
bio-vcf	Smart VCF parser bio-vcf-0.9.2	0.9.2, 0.9.2
bioconductor-dada2	Accurate, high-resolution sample inference from amplicon sequencing data	1.14.0
biopet-seqstat	SeqStat is a package that contains tools to generate stats from a FastQ file, merge those stats for multiple samples, and validate the generated stats files.	1.0.1
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.	0.22.2
blast	BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.	2.2.31, 2.7.1, 2.9.0
bokeh	Statistical and novel interactive HTML plots for Python	1.4.0
bowtie	An ultrafast memory-efficient short read aligner	1.2.2, 1.2.3
bowtie2	Fast and sensitive read alignment	2.3.4.3, 2.3.5, 2.4.1
braker2	BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.	2.1.4
busco	BUSCO from QC to gene prediction and phylogenomics	4.0.5, 3.0.2
bustools	bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.	0.40.0
bwa	The BWA read mapper.	0.7.17
canu	Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.	1.8, 2.0, 1.6, 1.7, 1.7.1
cap3	CAP3 A DNA sequence assembly program cap3-10.2011	10.2011, 10.2011
ceas	CEAS Cis-regulatory Element Annotation System	1.0.2
cellranger	A set of analysis pipelines that perform sample demultiplexing, V(D)J transcript sequence assembly and annotation, gene expression and feature barcode analysis from Single Cell Immune Profiling data.	4.0.0
centrifuge	Classifier for metagenomic sequences.	1.0.4_beta
charger	Characterization of Germline variants	0.5.2, 0.5.4
circlator	circlator a tool to circularise genome assemblies	1.5.5, 1.5.0
clustalo	Latest version of Clustal a multiple sequence alignment program for DNA or proteins	1.2.4
compilers	A metapackage to obtain compilers	1.0.4
concoct	Clustering cONtigs with COverage and ComposiTion	1.1.0, 0.4.0
coreutils	The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.	8.25
crossmap	CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies.	0.3.9
cryolo	Deep learning particle picking procedure based YOLO.	1.7.4-gpu
csvkit	A suite of command-line tools for working with CSV, the king of tabular file formats	1.0.3
cufflinks	Transcriptome assembly and differential expression analysis for RNA-Seq.	2.2.1
cutadapt	Trim adapters from high-throughput sequencing reads	1.8.3, 1.10, 2.10, 1.16, 1.18, 2.3, 2.8
dadi	Fit population genetic models using diffusion approximations to the allele frequency spectrum	2.0.5
deeptools	A set of user-friendly tools for normalization and visualzation of deep-sequencing data	2.5.3, 3.1.2, 3.2.0, 3.5.0, 2.5.4
delly	Structural variant discovery by integrated paired-end and split-read analysis	0.7.9, 0.8.1, 0.8.3
diamond	Accelerated BLAST compatible local sequence aligner	0.9.22, 0.9.28, 0.9.36, 0.9.21
discasm	DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. - https //github.com/DISCASM/DISCASM/wiki	0.1.3
discosnp	Designed for discovering all kinds of SNPs	2.3.0, 2.4.3
dropseq_tools	Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab	2.3.0
emboss	The European Molecular Biology Open Software Suite	6.6.0
enabrowsertools	A collection of scripts to assist in the retrieval of data from the ENA Browser	1.5.4
ensembl-vep	Ensembl Variant Effect Predictor	98.2
epa-ng	Massively parallel phylogenetic placement of genetic sequences	0.3.6, 0.2.1, 0.3.5
epic2	ChIP-seq broad peak calling tool, meant to be easier to use and more performant than SICER	0.0.41
exonerate	Exonerate - A generic tool for pairwise sequence comparison / alignment	2.4.0
fastme		2.1.5
fastp	A FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)	0.20.0, 0.12.5
fastq-screen	FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect	0.13.0
fastqc	A quality control tool for high throughput sequence data.	0.11.5, 0.11.7, 0.11.8, 0.11.9
fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences	2.1.10
fastx_toolkit	The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.	0.0.14
filtlong	Filtlong is a tool for filtering long reads by quality	0.2.0
flye	Fast and accurate de novo assembler for single molecule sequencing reads	2.6
freebayes	Bayesian haplotype-based polymorphism discovery and genotyping	1.2.0
frogs	FROGS is a workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data. This is the official release 3.1.0 of FROGS.	3.1.0, 2.0.1
gappa	Genesis Applications for Phylogenetic Placement Analysis	0.5.1, 0.4.0
gatk4	Genome Analysis Toolkit (GATK4)	4.0.10.0, 4.1.4.1, 4.1.7.0
gautomatch	Fully automatic acccurate, convenient and extremely fast particle picking for EM	0.56_sm62_cu8.0
gblocks	Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.	0.91b
gcc	GNU C C++ and Fortran Compiler	7.3.0, 7.5.0, 8.4.0, 9.3.0
gmap-fusion	GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.	0.4.0
gmap	Genomic mapping and alignment program for mRNA and EST sequences.	2020.06.01
graphviz	Open Source graph visualization software.	2.40.1
gridss	GRIDSS a Genomic Rearrangement IDentification Software Suite	1.9.0
gromacs	GROMACS is a versatile package to perform molecular dynamics.	2020.2
h5py	Read and write HDF5 files from Python	2.10.0
hicstuff	General purpose stuff to generate and handle Hi-C data in its simplest form.	2.3.0
hisat2	graph-based alignment of next generation sequencing reads to a population of genomes	2.1.0
hmmer	Biosequence analysis using profile hidden Markov models	3.2.1
hmmlearn	Hidden Markov Models in Python with scikit-learn like API.	0.2.4
homer	Software for motif discovery and next generation sequencing analysis	4.9.1, 4.10, 4.11
htseq	HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.	0.9.1, 0.11.2
htslib	C library for high-throughput sequencing data formats.	1.7, 1.9
humann	HUMAnN The HMP Unified Metabolic Analysis Network, version 3	3.0.0.alpha.3
idr	The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.	2.0.4.2
instagraal	instaGRAAL is a large genome reassembler based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.	0.1.2
isoseq3	Scalable de novo isoform discovery	3.3.0
java-jdk	The Zulu OpenJDK build.	8.0.112
jpredapi	Python library for submitting jobs to JPRED - A Protein Secondary Structure Prediction Server	1.5.6
kaiju	Fast and sensitive taxonomic classification for metagenomics	1.7.3
kallisto	Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.	0.44.0, 0.46.2
keras	Deep Learning for Python	2.2.4
kraken2	Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.	2.0.9beta, 2.0.7_beta, 2.0.8_beta
lima	Demultiplex barcoded samples	1.11.0
links	Long Interval Nucleotide K-mer Scaffolder	1.8.7
longqc	LongQC is a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities sample qc and platform qc.	1.1.1
lordec	A hybrid error correction program for long, PacBio reads	0.9
lumpy-sv	a general probabilistic framework for structural variant discovery	0.3.0
macs2	Model Based Analysis for ChIP-Seq data	2.1.1.20160309, 2.2.7.1
mafft	Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform	7.407, 7.313
maker	MAKER is a portable and easily configurable genome annotation pipeline.	2.31.10, 2.31.8
manta	Structural variant and indel caller for mapped sequencing data	1.4.0
mapdamage2	mapDamage tracking and quantifying damage patterns in ancient DNA sequences http //geogenetics.ku.dk/all_literature/mapdamage/	2.0.8
masurca	MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software.	3.3.4, 3.3.5, 3.4.1, 3.3.1, 3.3.3
mcclintock	Meta-pipeline to identify transposable element insertions using next generation sequencing data	master
medaka	Neural network sequence error correction.	1.0.3
megahit	MEGAHIT An ultra-fast single-node solution for large and complex	1.2.9, 1.2.8
megan	A tool for studying the taxonomic content of a set of DNA reads	6.12.3
mercat	Mercat a versatile counter and diversity estimator for data base independent property analysis obtained from whole community sequencing data.	0.2
metabat2	Metagenome binning	2.14
mgltools	MGLTools is an program for visualization and analisys of molecular structures.	1.5.6
midas	An integrated pipeline for estimating strain-level genomic variation from metagenomic data	1.3.2, 1.2.2
migrate-n	Population Genetics - Panmixia and Migration detection	3.6.11, 4.4.4
minimap2	A versatile pairwise aligner for genomic and spliced nucleotide sequences.	2.13, 2.17, 2.14
mir-prefer	miR-PREFeR microRNA PREdiction From small RNAseq data	0.24
mirdeep2	A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs	2.0.1.2
mmseqs2	MMseqs2.0 ultra fast and sensitive sequence search and clustering suite	8.fac81, 10.6d92c, 11.e1a1c, 8-fac81, 10-6d92c
mosdepth	Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.	0.2.3, 0.2.6
mothur	This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.	1.41.0, 1.44.11, 1.42.0
motus	Marker gene-based OTU (mOTU) profiling	2.5.1
mrbayes	Bayesian Inference of Phylogeny	3.2.6
msprime	A fast and accurate coalescent simulator.	0.7.3
multiqc	Create aggregate bioinformatics analysis reports across many samples and tools	1.6, 1.7, 1.9, 1.3, 1.5
music	MUltiScale enrIchment Calling for ChIP-Seq Datasets	1.0.0
nanofilt	Filtering and trimming of Oxford Nanopore Sequencing data	2.7.1
nemo-age	In Nemo-age, it is possible to model genetic and phenotypic evolution in populations with, for instance, overlapping generations, a seed bank, and multiple age classes with stage-specific transition rates, fecundities, selection pressures, and dispersal rates, among other things.	0.29.0
nextflow	A DSL for data-driven computational pipelines http //nextflow.io	18.10.1, 20.04.1, 0.27.6
obitools	The OBITools package is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information	1.2.11, 3.0.0_beta5, 1.0.010, 1.2.10
openmpi	An open source Message Passing Interface implementation.	4.0.4
orffinder	ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation.	0.4.3
orthofinder	Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!	2.3.3, 1.1.10, 2.2.0, 2.2.6
pandoc	Universal markup converter (repackaged binaries)	2.7.2
parallel	GNU parallel is a shell tool for executing jobs in parallel using one or more computers.	20190322, 20190722
pasa	PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.	2.4.1, 2.3.3, 2.3.3.bioconda
pb-assembly	Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin)	0.0.2, 0.0.0
pb-falcon	FALCON/Unzip tool-suite (originally by Jason Chin)	0.2.4
pbcoretools	CLI tools and add-ons for PacBio's core APIs	0.8.1
pbmm2	A minimap2 frontend for PacBio native data formats	1.3.0
pbsv	pbsv - PacBio structural variant (SV) calling and analysis tools	2.0.2
pdfgrep	A commandline utility to search text in PDF files	2.1.2
perl-dbd-sqlite	Self Contained RDBMS in a DBI Driver	1.6.4
perl-vcftools-vcf	cpanm ready distribution of VCFtools Perl libraries	0.1.16
perl	The Perl programming language interpreter + some libraries perl-5.26.2	5.26.2, 5.26.2
pgdspider	An automated data conversion tool for connecting population genetics and genomics programs	2.1.1.5
phame	A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.	1.0.3
phantompeakqualtools	This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.	1.2, 1.2.2
phylobayes	PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.	4.1c
phyml	Phylogenetic estimation using (Maximum) Likelihood	3.3.20180621, 3.3.20190909
picard	Java tools for working with NGS data in the BAM format	2.10.6, 2.18.9, 2.22.0, 2.23.5
picrust	PICRUSt Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	1.1.3
picrust2	PICRUSt Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	2.1.1_b
pigz	parallel implementation of gzip that exploits multiple processors and multiple cores to the hilt when compressing data	2.3.4
pilon	Pilon is an automated genome assembly improvement and variant detection tool.	1.23, 1.22
pindel	Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data	0.2.5b9
pipmir	PIPmiR algorithm - identify novel plant miRNA genes from a combination of deep sequencing data and genomic features.	1.1
plink	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	1.90b4, 1.90b6.18
plink2	Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	2.00a2.3
porechop	Adapter removal and demultiplexing of Oxford Nanopore reads	0.2.3_seqan2.1.1
ppanggolin	PPanGGOLiN Depicting microbial species diversity via a Partitioned PanGenome Graph	1.0.1
prodigal	Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program	2.6.3
prokka	Rapid annotation of prokaryotic genomes	1.14.6, 1.13, 1.13.4
psipred	Accurate protein secondary structure prediction	4.01
pyega3	EGA python client	3.0.39
pygtftk	The gtftk suite providing facilities to manipulate genomic annotations in gtf format.	1.2.2
pypy	PyPy is a Python interpreter and just-in-time compiler.	2.7-5.10.0, 3.5-7.0.0
pyscenic	A lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data	0.9.19, 0.10.0
python	Python is an interpreted, high-level, general-purpose programming language. This env comes with the most common libraries. python-3.7	2.7, 3.7, 2.7, 3.7
qiime2	QIIME 2™ is a next-generation microbiome bioinformatics platform	2019.1.0, 2017.10, 2017.12, 2018.2, 2018.4, 2018.6, 2018.8, 2019.4, 2019.7
qualimap	Quality control of alignment sequencing data and its derivatives like feature counts	2.2.2b
quast	Quality Assessment Tool for Genome Assemblies	5.0.2
r-eacon	Easy Copy Number. EaCoN aims to be an all-packed in, user-friendly solution to perform relative or absolute copy-number analysis for multiple sources of data, with three different segmenters available (and corresponding three copy-number modelization methods)	0.3.4_1
r	R is a free software environment for statistical computing and graphics.	3.5.1, 3.6.3, 4.0.0, 4.0.2, 3.5.1-bk, 3.6.1, 3.6.2
raxml-ng	RAxML Next Generation faster, easier-to-use and more flexible	0.9.0
raxml	Phylogenetics - Randomized Axelerated Maximum Likelihood.	8.2.12
relion	Relion is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)	3.0.7
repet	The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale.	3.0, 2.5
rnaquast	rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.	1.5.1
roary	Rapid large-scale prokaryote pan genome analysis	3.12.0
rsem	RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute's Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.	1.3.2
rseqc	RNA-seq QC Package	2.6.4
rstudio-server	RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server	1.2.5042
salmon	Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment	0.11.3, 0.14.1, 0.14.2, 1.3.0, 0.14.0
sambamba	Tools for working with SAM/BAM data	0.7.1
sample	R is a free software environment for statistical computing and graphics.	2.13.1, 3.5.1
samtools	Tools for dealing with SAM, BAM and CRAM files	1.3.1, 1.5, 1.9, 1.10, 1.6
scikit-allel	A Python package for exploring and analysing genetic variation data.	1.2.1
scikit-learn	Scikit-learn is an open source machine learning library.	0.22.1
screen	Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells	4.8.0
seqtk	Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format	1.3
shortstack	ShortStack Comprehensive annotation and quantification of small RNA genes	3.8.5
sicer	A clustering approach for identification of enriched domains from histone modification ChIP-Seq data sicer-1.1	1.1, 1.1
sickle-trim	Windowed Adaptive Trimming for fastq files using quality	1.33
signalp	The SignalP 5.0 server predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya.	5.0
simka	Simka and simkaMin are de novo comparative metagenomics tools. Simka represents each dataset as a k-mer spectrum and computes several classical ecological distances between them. SimkaMin outputs approximate (but very similar) results by subsampling the kmer space and requires much less computational resources.	1.5.2, 1.4.0, 1.5.0
singularity		NA	NA
snakemake	A popular workflow management system aiming at full in-silico reproducibility.	5.3.0, 5.7.4, 5.19.2, 3.8.2, 3.12.0, 4.1.0, 5.2.0
sniffles	Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)	1.0.10, 1.0.11
snippy	Rapid bacterial SNP calling and core genome alignments	4.3.3
snpeff	Genetic variant annotation and effect prediction toolbox	4.3.1t
snpsift	Toolbox that allows you to filter and manipulate annotated files	4.3.1t
sortmerna	SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.	2.1b, 4.2.0
spades	SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.	3.13.1, 3.14.1
sparcc	SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).	0.1.0
sqlite	Implements a self-contained, zero-configuration, SQL database engine	3.30.1
sra-tools	SRA Toolkit and SDK from NCBI	2.10.0, 2.10.3
stacks	Stacks is a software pipeline for building loci from RAD-seq	2.3d, 2.5, 2.52, 1.47, 2.0, 2.0Beta7c, 2.0Beta8, 2.0Beta8c, 2.0Beta9, 2.0Beta10a, 2.1, 2.2, 2.3, 2.3b, 2.4
star	An RNA-seq read aligner.	2.6, 2.7.2b, 2.7.5a, 2.7.1a
stream	STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http //stream.pinellolab.org	0.4.1, 1.0, 20180425
stringtie	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.	2.1.2
structure	The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.	2.3.4
subread	High-performance read alignment, quantification, and mutation discovery	1.6.1, 2.0.1
swarm	A robust and fast clustering method for amplicon-based studies.	3.0.0
targetp	TargetP-2.0 server predicts the presence of N-terminal presequences signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.	2.0
tetools-l	compute RNA read count for transposable elements and Differential expression analysis of transposable elements	1.0.0
tetools	Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg	1.2
texlive	An easy way to get up and running with the TeX document production system	2019, 20180414
tk	A dynamic programming language with GUI support. Bundles Tcl and Tk.	8.6.10
tmux	A terminal multiplexer.	3.1
toil	A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python	3.14.0
topaz	A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models.	0.2.4
tophat	A spliced read mapper for RNA-Seq	2.1.1
tremolo	Transposable Elements MOvement detection using LOng reads	0.1
trim-galore	Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control	0.5.0, 0.6.5
trimal		1.4.1
trimmomatic	A flexible read trimming tool for Illumina NGS data	0.36, 0.39
trinity	Trinity assembles transcript sequences from Illumina RNA-Seq data.	2.8.4, 2.8.5, 2.9.1, 2.11.0, 2.5.1, 2.9.1
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 trinotate-3.2.0	3.2.0, 3.2.0
ucsc-bedgraphtobigwig	Convert a bedGraph file to bigWig format.	377
ucsc-bedsort	Sort a .bed file by chrom,chromStart.	377
ucsc-bigwigtowig	Convert bigWig to wig. This will keep more of the same structure of the	377
ucsc-fatotwobit	Convert DNA from fasta to 2bit format	377
umap-learn	Uniform Manifold Approximation and Projection	0.4.6
umi_tools	Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)	1.0.1
unicycler	Hybrid assembly pipeline for bacterial genomes	0.4.8, 0.4.1, 0.4.3, 0.4.4
varscan	variant detection in massively parallel sequencing data	2.4.3, 2.4.4
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	0.1.16, 0.1.15
velocyto.py	A library for the analysis of RNA velocity.	0.17.17
virsorter	Mining viral signal from microbial genomic data.	1.0.6, virsorter
vsearch	a versatile open source tool for metagenomics (USEARCH alternative)	2.14.1, 2.13.1
wtdbg	Wtdbg2 A fuzzy Bruijn graph approach to long noisy reads assembly	2.5
xgboost	Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for	0.82
3d-dna	3d-dna-20180717	20180717
ale	ale-20180904	20180904
antismash	antismash-4.1.0	4.1.0
arb	arb-6.0.6	6.0.6
barrnap	barrnap-0.9	0.9
base	base-base	base
bbmap	bbmap-38.22	38.22
beagle	beagle-5.1_24Aug19.3e8	5.1_24Aug19.3e8
beast	beast-1.10.1	1.10.1
beast2	beast2-2.5.0	2.5.0
besst	besst-2.2.7	2.2.7
bioconductor-rots	bioconductor-rots-1.0.0	1.0.0
biokevlar		0.6.1
blasr	blasr-5.2p1	5.2p1
blobtools	blobtools-1.0.1	1.0.1
bracken	bracken-2.2	2.2
breseq		0.35.0
cd-hit	cd-hit-4.8.1	4.8.1
checkm	checkm-1.0.11	1.0.7, 1.0.11
circos	circos-0.69.6	0.69.6
clc-assembly-cell	clc-assembly-cell-5.1.1	3.2.2, 4.0.12, 4.1.0, 5.0.5, 5.1.0, 5.1.1
cocacola	cocacola-20170305	20170305
consel	consel-0.20	0.20
egglib	egglib-3.0.0b21	3.0.0b21
eggnog-mapper	eggnog-mapper-1.0.3	1.0.3
emirge	emirge-0.61.1	0.61.1
encode-blacklist	encode-blacklist-2.0	2.0
entrez-direct	entrez-direct-11.0	11.0
ete3	ete3-3.1.1	3.0.0, 3.1.1
faststructure		1.0
fineradstructure	fineradstructure-0.3.2r109	0.3.2r109
gatb-minia-pipeline	gatb-minia-pipeline-20171215	20171215
gatk	gatk-4.0.21	3.8, 4.0.21
gcta	gcta-1.26.0	1.26.0
hicaptools	hicaptools-1.3.0	1.3.0
hmmer2go	hmmer2go-0.17.8	0.17.8
ics	ics-2018	2018
infernal	infernal-1.1.2	1.1.2
ipyrad	ipyrad-0.9.8	0.9.8
iqtree	iqtree-1.6.8	1.6.8
krakenuniq	krakenuniq-0.5.8	0.5.8
lefse	lefse-1.0.8.post1	1.0.8.post1
macs		1.4.3
maker-mpi	maker-mpi-2.31.8	2.31.8
marker	marker-2.31.8	2.31.8
matam	matam-1.5.3	1.3.0, 1.5.0, 1.5.1, 1.5.2, 1.5.3
maxbin2	maxbin2-2.2.6	2.2.6
miniasm	miniasm-0.3_r179	0.3_r179
miphy	miphy-0.9.2	0.9.2
mira	mira-4.9.6	3.4.1.1, 4.0.2, 4.9.6
mixcr		2.1.10
modeltest-ng	modeltest-ng-0.1.15	0.1.15
modulefile.template	__name__-__version__	NA
molpopgen-analysis	molpopgen-analysis-0.8.8	0.8.8
muscle		3.8.1551
netevo	netevo-2018	2018
networkx	networkx-2.3	2.3
ngmerge	ngmerge-0.3	0.3
paprica	paprica-0.4.0e	0.4.0e
phyloligo	phyloligo-2017.07.12	2017.07.12
plass	plass-2.c7e35	2.c7e35
platypus-variant	platypus-variant-0.8.1.2	0.8.1.2
prinseq	prinseq-0.20.4	0.20.4
proovread	proovread-2.14.0	2.14.0
qiime	qiime-1.9.1	1.9.1
qushape	qushape-1.0	1.0
r-sartools	r-sartools-1.5.1	1.5.1
r-sleuth	r-sleuth-0.30.0	0.30.0
racon	racon-1.3.1	1.3.1
radsex	radsex-20180214	0.2.0, 20180214
repeatmasker		4.0.8, 4.0.9_p2
sdm	sdm-2018	2018
tbl2asn	tbl2asn-25.3	25.3
tracy	tracy-0.5.5	0.5.5
transdecoder	transdecoder-5.5.0	5.0.2, 5.5.0
trifusion	trifusion-1.0.0.post2	1.0.0.post2
trnascan-se	trnascan-se-2.0	2.0
umap	umap-1.1.1	1.1.1
winstoncleaner	winstoncleaner-20180403	20180403