_genome2-legacymany 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 
abyssAssembly By Short Sequences - a de novo, parallel, paired-end sequence assembler2.2.1Bioconda GitLab
adxvadxv can be used to display and analyze 2-D area detector data. It is optimized to display X-Ray crystallography diffraction images.1.9.14Singularity GitLab
alientrimmerTrimmer of contaminant oligonucleotide sequences such as primers and adapters0.4.1Conda GitLab
anvioAn interactive analysis and visualization platform for omics data6.1, 4.0.0, 5.2.0, 5.5.0, 6.0.0Bioconda GitLab
arcsScaffolding genome sequence assemblies using 10X Genomics data1.1.0Bioconda GitLab
assemblyticsanalyze a genome assembly by comparing it to a reference genome1.2.1Bioconda GitLab
augustusAUGUSTUS 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, 3.3.2Bioconda GitLab
bam2fastxConverting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files1.3.0Bioconda GitLab
bcbc is an arbitrary precision numeric processing language.1.07.1Conda GitLab
bcftoolsBCFtools 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, 1.6Bioconda GitLab
bcl2fastqThe Illumina bcl2fastq2 Conversion Software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.2.20.0Singularity GitLab
bedtoolsA powerful toolset for genome arithmetic2.26.0, 2.27.1, 2.29.2Bioconda GitLab
berokkaTrim, circularise and orient long read bacterial genome assemblies.0.2.3Bioconda GitLab
bio-vcfSmart VCF parser bio-vcf-, 0.9.2Bioconda GitLab
bioconductor-dada2Accurate, high-resolution sample inference from amplicon sequencing data1.14.0Bioconda GitLab
biopet-seqstatSeqStat 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.1.0.1Bioconda GitLab
bismarkBismark 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.0.22.2Bioconda GitLab
blastBLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.2.2.31, 2.7.1, 2.9.0Bioconda GitLab
bokehStatistical and novel interactive HTML plots for Python1.4.0Conda GitLab
bowtieAn ultrafast memory-efficient short read aligner1.2.2, 1.2.3Bioconda GitLab
bowtie2Fast and sensitive read alignment2.3.4.3, 2.3.5, 2.4.1Bioconda GitLab
braker2BRAKER2 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.2.1.4Bioconda GitLab
buscoBUSCO from QC to gene prediction and phylogenomics4.0.5, 3.0.2Bioconda GitLab
bustoolsbustools is a program for manipulating BUS files for single cell RNA-Seq datasets.0.40.0Bioconda GitLab
bwaThe BWA read mapper.0.7.17Bioconda GitLab
canuCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing.1.8, 2.0, 1.6, 1.7, 1.7.1Bioconda GitLab
cap3CAP3 A DNA sequence assembly program cap3-10.201110.2011, 10.2011Bioconda GitLab
ceasCEAS Cis-regulatory Element Annotation System1.0.2Bioconda GitLab
cellrangerA 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.4.0.0Singularity GitLab
centrifugeClassifier for metagenomic sequences.1.0.4_betaBioconda GitLab
chargerCharacterization of Germline variants0.5.2, 0.5.4Conda GitLab
circlatorcirclator a tool to circularise genome assemblies1.5.5, 1.5.0Bioconda GitLab
clustaloLatest version of Clustal a multiple sequence alignment program for DNA or proteins1.2.4Bioconda GitLab
compilersA metapackage to obtain compilers1.0.4Conda GitLab
concoctClustering cONtigs with COverage and ComposiTion1.1.0, 0.4.0Bioconda GitLab
coreutilsThe 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.8.25Conda GitLab
crossmapCrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies.0.3.9Bioconda GitLab
cryoloDeep learning particle picking procedure based YOLO.1.7.4-gpuSingularity GitLab
csvkitA suite of command-line tools for working with CSV, the king of tabular file formats1.0.3Conda GitLab
cufflinksTranscriptome assembly and differential expression analysis for RNA-Seq.2.2.1Bioconda GitLab
cutadaptTrim adapters from high-throughput sequencing reads1.8.3, 1.10, 2.10, 1.16, 1.18, 2.3, 2.8Bioconda GitLab
dadiFit population genetic models using diffusion approximations to the allele frequency spectrum2.0.5Conda GitLab
deeptoolsA set of user-friendly tools for normalization and visualzation of deep-sequencing data2.5.3, 3.1.2, 3.2.0, 3.5.0, 2.5.4Bioconda GitLab
dellyStructural variant discovery by integrated paired-end and split-read analysis0.7.9, 0.8.1, 0.8.3Bioconda GitLab
diamondAccelerated BLAST compatible local sequence aligner0.9.22, 0.9.28, 0.9.36, 0.9.21Bioconda GitLab
discasmDISCASM 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 // GitLab
discosnpDesigned for discovering all kinds of SNPs2.3.0, 2.4.3Bioconda GitLab
dropseq_toolsPackage for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab2.3.0Bioconda GitLab
embossThe European Molecular Biology Open Software Suite6.6.0Bioconda GitLab
enabrowsertoolsA collection of scripts to assist in the retrieval of data from the ENA Browser1.5.4Bioconda GitLab
ensembl-vepEnsembl Variant Effect Predictor98.2Bioconda GitLab
epa-ngMassively parallel phylogenetic placement of genetic sequences0.3.6, 0.2.1, 0.3.5Bioconda GitLab
epic2ChIP-seq broad peak calling tool, meant to be easier to use and more performant than SICER0.0.41Bioconda GitLab
exonerateExonerate - A generic tool for pairwise sequence comparison / alignment2.4.0Bioconda GitLab
fastme2.1.5Bioconda GitLab
fastpA FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)0.20.0, 0.12.5Bioconda GitLab
fastq-screenFastQ 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 expect0.13.0Bioconda GitLab
fastqcA quality control tool for high throughput sequence data.0.11.5, 0.11.7, 0.11.8, 0.11.9Bioconda GitLab
fasttreeFastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences2.1.10Bioconda GitLab
fastx_toolkitThe FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.0.0.14Bioconda GitLab
filtlongFiltlong is a tool for filtering long reads by quality0.2.0Bioconda GitLab
flyeFast and accurate de novo assembler for single molecule sequencing reads2.6Bioconda GitLab
freebayesBayesian haplotype-based polymorphism discovery and genotyping1.2.0Bioconda GitLab
frogsFROGS 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, 2.0.1Bioconda GitLab
gappaGenesis Applications for Phylogenetic Placement Analysis0.5.1, 0.4.0Bioconda GitLab
gatk4Genome Analysis Toolkit (GATK4),, GitLab
gautomatchFully automatic acccurate, convenient and extremely fast particle picking for EM0.56_sm62_cu8.0Singularity GitLab
gblocksSelection of conserved blocks from multiple alignments for their use in phylogenetic analysis.0.91bBioconda GitLab
gccGNU C C++ and Fortran Compiler7.3.0, 7.5.0, 8.4.0, 9.3.0Conda GitLab
gmap-fusionGMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly.0.4.0Bioconda GitLab
gmapGenomic mapping and alignment program for mRNA and EST sequences.2020.06.01Bioconda GitLab
graphvizOpen Source graph visualization software.2.40.1Conda GitLab
gridssGRIDSS a Genomic Rearrangement IDentification Software Suite1.9.0Bioconda GitLab
gromacsGROMACS is a versatile package to perform molecular dynamics.2020.2Bioconda GitLab
h5pyRead and write HDF5 files from Python2.10.0Conda GitLab
hicstuffGeneral purpose stuff to generate and handle Hi-C data in its simplest form.2.3.0Bioconda GitLab
hisat2graph-based alignment of next generation sequencing reads to a population of genomes2.1.0Bioconda GitLab
hmmerBiosequence analysis using profile hidden Markov models3.2.1Bioconda GitLab
hmmlearnHidden Markov Models in Python with scikit-learn like API.0.2.4Conda GitLab
homerSoftware for motif discovery and next generation sequencing analysis4.9.1, 4.10, 4.11Bioconda GitLab
htseqHTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.0.9.1, 0.11.2Bioconda GitLab
htslibC library for high-throughput sequencing data formats.1.7, 1.9Bioconda GitLab
humannHUMAnN The HMP Unified Metabolic Analysis Network, version 33.0.0.alpha.3Conda GitLab
idrThe 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. GitLab
instagraalinstaGRAAL is a large genome reassembler based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.0.1.2Singularity GitLab
isoseq3Scalable de novo isoform discovery3.3.0Bioconda GitLab
java-jdkThe Zulu OpenJDK build.8.0.112Conda GitLab
jpredapiPython library for submitting jobs to JPRED - A Protein Secondary Structure Prediction Server1.5.6Bioconda GitLab
kaijuFast and sensitive taxonomic classification for metagenomics1.7.3Bioconda GitLab
kallistoQuantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.0.44.0, 0.46.2Bioconda GitLab
kerasDeep Learning for Python2.2.4Conda GitLab
kraken2Kraken2 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_betaBioconda GitLab
limaDemultiplex barcoded samples1.11.0Bioconda GitLab
linksLong Interval Nucleotide K-mer Scaffolder1.8.7Bioconda GitLab
longqcLongQC 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.1.1.1Singularity GitLab
lordecA hybrid error correction program for long, PacBio reads0.9Bioconda GitLab
lumpy-sva general probabilistic framework for structural variant discovery0.3.0Bioconda GitLab
macs2Model Based Analysis for ChIP-Seq data2.1.1.20160309, GitLab
mafftMultiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform7.407, 7.313Bioconda GitLab
makerMAKER is a portable and easily configurable genome annotation pipeline.2.31.10, 2.31.8Bioconda GitLab
mantaStructural variant and indel caller for mapped sequencing data1.4.0Bioconda GitLab
mapdamage2mapDamage tracking and quantifying damage patterns in ancient DNA sequences http // GitLab
masurcaMaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software.3.3.4, 3.3.5, 3.4.1, 3.3.1, 3.3.3Bioconda GitLab
mcclintockMeta-pipeline to identify transposable element insertions using next generation sequencing datamasterSingularity GitLab
medakaNeural network sequence error correction.1.0.3Bioconda GitLab
megahitMEGAHIT An ultra-fast single-node solution for large and complex1.2.9, 1.2.8Bioconda GitLab
meganA tool for studying the taxonomic content of a set of DNA reads6.12.3Bioconda GitLab
mercatMercat a versatile counter and diversity estimator for data base independent property analysis obtained from whole community sequencing data.0.2Bioconda GitLab
metabat2Metagenome binning2.14Bioconda GitLab
mgltoolsMGLTools is an program for visualization and analisys of molecular structures.1.5.6Bioconda GitLab
midasAn integrated pipeline for estimating strain-level genomic variation from metagenomic data1.3.2, 1.2.2Bioconda GitLab
migrate-nPopulation Genetics - Panmixia and Migration detection3.6.11, 4.4.4Singularity GitLab
minimap2A versatile pairwise aligner for genomic and spliced nucleotide sequences.2.13, 2.17, 2.14Bioconda GitLab
mir-prefermiR-PREFeR microRNA PREdiction From small RNAseq data0.24Bioconda GitLab
mirdeep2A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs2.0.1.2Bioconda GitLab
mmseqs2MMseqs2.0 ultra fast and sensitive sequence search and clustering suite8.fac81, 10.6d92c, 11.e1a1c, 8-fac81, 10-6d92cBioconda GitLab
mosdepthFast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.0.2.3, 0.2.6Bioconda GitLab
mothurThis 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, 1.42.0Bioconda GitLab
motusMarker gene-based OTU (mOTU) profiling2.5.1Bioconda GitLab
mrbayesBayesian Inference of Phylogeny3.2.6Bioconda GitLab
msprimeA fast and accurate coalescent simulator.0.7.3Conda GitLab
multiqcCreate aggregate bioinformatics analysis reports across many samples and tools1.6, 1.7, 1.9, 1.3, 1.5Bioconda GitLab
musicMUltiScale enrIchment Calling for ChIP-Seq Datasets1.0.0Bioconda GitLab
nanofiltFiltering and trimming of Oxford Nanopore Sequencing data2.7.1Bioconda GitLab
nemo-ageIn 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.0.29.0Bioconda GitLab
nextflowA DSL for data-driven computational pipelines http //nextflow.io18.10.1, 20.04.1, 0.27.6Bioconda GitLab
obitoolsThe OBITools package is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information1.2.11, 3.0.0_beta5, 1.0.010, 1.2.10Bioconda GitLab
openmpiAn open source Message Passing Interface implementation.4.0.4Conda GitLab
orffinderORF 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.0.4.3Singularity GitLab
orthofinderAccurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!2.3.3, 1.1.10, 2.2.0, 2.2.6Bioconda GitLab
pandocUniversal markup converter (repackaged binaries)2.7.2Conda GitLab
parallelGNU parallel is a shell tool for executing jobs in parallel using one or more computers.20190322, 20190722Conda GitLab
pasaPASA, 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.biocondaBioconda GitLab
pb-assemblyMeta-package for Falcon/Unzip tool-suite (originally by Jason Chin)0.0.2, 0.0.0Bioconda GitLab
pb-falconFALCON/Unzip tool-suite (originally by Jason Chin)0.2.4Bioconda GitLab
pbcoretoolsCLI tools and add-ons for PacBio's core APIs0.8.1Bioconda GitLab
pbmm2A minimap2 frontend for PacBio native data formats1.3.0Bioconda GitLab
pbsvpbsv - PacBio structural variant (SV) calling and analysis tools2.0.2Bioconda GitLab
pdfgrepA commandline utility to search text in PDF files2.1.2Conda GitLab
perl-dbd-sqliteSelf Contained RDBMS in a DBI Driver1.6.4Bioconda GitLab
perl-vcftools-vcfcpanm ready distribution of VCFtools Perl libraries0.1.16Bioconda GitLab
perlThe Perl programming language interpreter + some libraries perl-, 5.26.2Conda GitLab
pgdspiderAn automated data conversion tool for connecting population genetics and genomics programs2.1.1.5Bioconda GitLab
phameA tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.1.0.3Bioconda GitLab
phantompeakqualtoolsThis 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, 1.2.2Bioconda GitLab
phylobayesPhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments.4.1cSingularity GitLab
phymlPhylogenetic estimation using (Maximum) Likelihood3.3.20180621, 3.3.20190909Bioconda GitLab
picardJava tools for working with NGS data in the BAM format2.10.6, 2.18.9, 2.22.0, 2.23.5Bioconda GitLab
picrustPICRUSt Phylogenetic Investigation of Communities by Reconstruction of Unobserved States1.1.3Bioconda GitLab
picrust2PICRUSt Phylogenetic Investigation of Communities by Reconstruction of Unobserved States2.1.1_bBioconda GitLab
pigzparallel implementation of gzip that exploits multiple processors and multiple cores to the hilt when compressing data2.3.4Conda GitLab
pilonPilon is an automated genome assembly improvement and variant detection tool.1.23, 1.22Bioconda GitLab
pindelPindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data0.2.5b9Bioconda GitLab
pipmirPIPmiR algorithm - identify novel plant miRNA genes from a combination of deep sequencing data and genomic features.1.1Bioconda GitLab
plinkWhole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.1.90b4, 1.90b6.18Bioconda GitLab
plink2Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.2.00a2.3Bioconda GitLab
porechopAdapter removal and demultiplexing of Oxford Nanopore reads0.2.3_seqan2.1.1Bioconda GitLab
ppanggolinPPanGGOLiN Depicting microbial species diversity via a Partitioned PanGenome Graph1.0.1Bioconda GitLab
prodigalProdigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program2.6.3Bioconda GitLab
prokkaRapid annotation of prokaryotic genomes1.14.6, 1.13, 1.13.4Bioconda GitLab
psipredAccurate protein secondary structure prediction4.01Conda GitLab
pyega3EGA python client3.0.39Bioconda GitLab
pygtftkThe gtftk suite providing facilities to manipulate genomic annotations in gtf format.1.2.2Bioconda GitLab
pypyPyPy is a Python interpreter and just-in-time compiler.2.7-5.10.0, 3.5-7.0.0Conda GitLab
pyscenicA 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 data0.9.19, 0.10.0Conda GitLab
pythonPython is an interpreted, high-level, general-purpose programming language. This env comes with the most common libraries. python-3.72.7, 3.7, 2.7, 3.7Conda GitLab
qiime2QIIME 2™ is a next-generation microbiome bioinformatics platform2019.1.0, 2017.10, 2017.12, 2018.2, 2018.4, 2018.6, 2018.8, 2019.4, 2019.7Conda GitLab
qualimapQuality control of alignment sequencing data and its derivatives like feature counts2.2.2bBioconda GitLab
quastQuality Assessment Tool for Genome Assemblies5.0.2Bioconda GitLab
r-eaconEasy 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_1Bioconda GitLab
rR 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, 3.6.2Conda GitLab
raxml-ngRAxML Next Generation faster, easier-to-use and more flexible0.9.0Bioconda GitLab
raxmlPhylogenetics - Randomized Axelerated Maximum Likelihood.8.2.12Bioconda GitLab
relionRelion 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)3.0.7Singularity GitLab
repetThe REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale.3.0, 2.5Singularity GitLab
rnaquastrnaQUAST 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.1.5.1Bioconda GitLab
roaryRapid large-scale prokaryote pan genome analysis3.12.0Bioconda GitLab
rsemRSEM 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.1.3.2Bioconda GitLab
rseqcRNA-seq QC Package2.6.4Bioconda GitLab
rstudio-serverRStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server1.2.5042Singularity GitLab
salmonHighly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment0.11.3, 0.14.1, 0.14.2, 1.3.0, 0.14.0Bioconda GitLab
sambambaTools for working with SAM/BAM data0.7.1Bioconda GitLab
sampleR is a free software environment for statistical computing and graphics.2.13.1, 3.5.1Conda GitLab
samtoolsTools for dealing with SAM, BAM and CRAM files1.3.1, 1.5, 1.9, 1.10, 1.6Bioconda GitLab
scikit-allelA Python package for exploring and analysing genetic variation data.1.2.1Conda GitLab
scikit-learnScikit-learn is an open source machine learning library.0.22.1Conda GitLab
screenScreen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells4.8.0Conda GitLab
seqtkSeqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format1.3Bioconda GitLab
shortstackShortStack Comprehensive annotation and quantification of small RNA genes3.8.5Bioconda GitLab
sicerA clustering approach for identification of enriched domains from histone modification ChIP-Seq data sicer-1.11.1, 1.1Bioconda GitLab
sickle-trimWindowed Adaptive Trimming for fastq files using quality1.33Bioconda GitLab
signalpThe 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.5.0Singularity GitLab
simkaSimka 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, 1.5.0Bioconda GitLab
singularityNANA GitLab
snakemakeA 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, 5.2.0Bioconda GitLab
snifflesSniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)1.0.10, 1.0.11Bioconda GitLab
snippyRapid bacterial SNP calling and core genome alignments4.3.3Bioconda GitLab
snpeffGenetic variant annotation and effect prediction toolbox4.3.1tBioconda GitLab
snpsiftToolbox that allows you to filter and manipulate annotated files4.3.1tBioconda GitLab
sortmernaSortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.2.1b, 4.2.0Singularity GitLab
spadesSPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.3.13.1, 3.14.1Bioconda GitLab
sparccSparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).0.1.0Bioconda GitLab
sqliteImplements a self-contained, zero-configuration, SQL database engine3.30.1Conda GitLab
sra-toolsSRA Toolkit and SDK from NCBI2.10.0, 2.10.3Bioconda GitLab
stacksStacks is a software pipeline for building loci from RAD-seq2.3d, 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, 2.4Bioconda GitLab
starAn RNA-seq read aligner.2.6, 2.7.2b, 2.7.5a, 2.7.1aBioconda GitLab
streamSTREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http //stream.pinellolab.org0.4.1, 1.0, 20180425Bioconda GitLab
stringtieStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.2.1.2Bioconda GitLab
structureThe 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.2.3.4Bioconda GitLab
subreadHigh-performance read alignment, quantification, and mutation discovery1.6.1, 2.0.1Bioconda GitLab
swarmA robust and fast clustering method for amplicon-based studies.3.0.0Bioconda GitLab
targetpTargetP-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.2.0Singularity GitLab
tetools-lcompute RNA read count for transposable elements and Differential expression analysis of transposable elements1.0.0Singularity GitLab
tetoolsDfam TE Tools includes RepeatMasker, RepeatModeler, and coseg1.2Singularity GitLab
texliveAn easy way to get up and running with the TeX document production system2019, 20180414Conda GitLab
tkA dynamic programming language with GUI support. Bundles Tcl and Tk.8.6.10Conda GitLab
tmuxA terminal multiplexer.3.1Conda GitLab
toilA scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python3.14.0Bioconda GitLab
topazA 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.0.2.4Singularity GitLab
tophatA spliced read mapper for RNA-Seq2.1.1Bioconda GitLab
tremoloTransposable Elements MOvement detection using LOng reads0.1Singularity GitLab
trim-galoreTrim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control0.5.0, 0.6.5Bioconda GitLab
trimal1.4.1Bioconda GitLab
trimmomaticA flexible read trimming tool for Illumina NGS data0.36, 0.39Bioconda GitLab
trinityTrinity assembles transcript sequences from Illumina RNA-Seq data.2.8.4, 2.8.5, 2.9.1, 2.11.0, 2.5.1, 2.9.1Bioconda GitLab
trinotateTrinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms trinotate-, 3.2.0Bioconda GitLab
ucsc-bedgraphtobigwigConvert a bedGraph file to bigWig format.377Bioconda GitLab
ucsc-bedsortSort a .bed file by chrom,chromStart.377Bioconda GitLab
ucsc-bigwigtowigConvert bigWig to wig. This will keep more of the same structure of the377Bioconda GitLab
ucsc-fatotwobitConvert DNA from fasta to 2bit format377Bioconda GitLab
umap-learnUniform Manifold Approximation and Projection0.4.6Conda GitLab
umi_toolsTools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)1.0.1Bioconda GitLab
unicyclerHybrid assembly pipeline for bacterial genomes0.4.8, 0.4.1, 0.4.3, 0.4.4Bioconda GitLab
varscanvariant detection in massively parallel sequencing data2.4.3, 2.4.4Bioconda GitLab
vcftoolsA 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 libraries0.1.16, 0.1.15Bioconda GitLab
velocyto.pyA library for the analysis of RNA velocity.0.17.17Bioconda GitLab
virsorterMining viral signal from microbial genomic data.1.0.6, virsorterBioconda GitLab
vsearcha versatile open source tool for metagenomics (USEARCH alternative)2.14.1, 2.13.1Bioconda GitLab
wtdbgWtdbg2 A fuzzy Bruijn graph approach to long noisy reads assembly2.5Bioconda GitLab
xgboostScalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for0.82Conda GitLab
checkmcheckm-, 1.0.11
clc-assembly-cellclc-assembly-cell-, 4.0.12, 4.1.0, 5.0.5, 5.1.0, 5.1.1
ete3ete3-, 3.1.1
gatkgatk-, 4.0.21
matammatam-, 1.5.0, 1.5.1, 1.5.2, 1.5.3
miramira-, 4.0.2, 4.9.6
radsexradsex-201802140.2.0, 20180214
repeatmasker4.0.8, 4.0.9_p2
transdecodertransdecoder-, 5.5.0