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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
alientrimmer | Trimmer of contaminant oligonucleotide sequences such as primers and adapters | 0.4.1 | ![GitLab GitLab](logo_gitlab.png) |
anvio | An interactive analysis and visualization platform for omics data | 6.1, 4.0.0, 5.2.0, 5.5.0, 6.0.0 | ![GitLab GitLab](logo_gitlab.png) |
arcs | Scaffolding genome sequence assemblies using 10X Genomics data | 1.1.0 | ![GitLab GitLab](logo_gitlab.png) |
assemblytics | analyze a genome assembly by comparing it to a reference genome | 1.2.1 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
bam2fastx | Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files | 1.3.0 | ![GitLab GitLab](logo_gitlab.png) |
bc | bc is an arbitrary precision numeric processing language. | 1.07.1 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
bcl2fastq | The Illumina bcl2fastq2 Conversion Software demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. | 2.20.0 | ![GitLab GitLab](logo_gitlab.png) |
bedtools | A powerful toolset for genome arithmetic | 2.26.0, 2.27.1, 2.29.2 | ![GitLab GitLab](logo_gitlab.png) |
berokka | Trim, circularise and orient long read bacterial genome assemblies. | 0.2.3 | ![GitLab GitLab](logo_gitlab.png) |
bio-vcf | Smart VCF parser
bio-vcf-0.9.2 | 0.9.2, 0.9.2 | ![GitLab GitLab](logo_gitlab.png) |
bioconductor-dada2 | Accurate, high-resolution sample inference from amplicon sequencing data | 1.14.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
blast | BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. | 2.2.31, 2.7.1, 2.9.0 | ![GitLab GitLab](logo_gitlab.png) |
bokeh | Statistical and novel interactive HTML plots for Python | 1.4.0 | ![GitLab GitLab](logo_gitlab.png) |
bowtie | An ultrafast memory-efficient short read aligner | 1.2.2, 1.2.3 | ![GitLab GitLab](logo_gitlab.png) |
bowtie2 | Fast and sensitive read alignment | 2.3.4.3, 2.3.5, 2.4.1 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
busco | BUSCO from QC to gene prediction and phylogenomics | 4.0.5, 3.0.2 | ![GitLab GitLab](logo_gitlab.png) |
bustools | bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. | 0.40.0 | ![GitLab GitLab](logo_gitlab.png) |
bwa | The BWA read mapper. | 0.7.17 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
cap3 | CAP3 A DNA sequence assembly program
cap3-10.2011 | 10.2011, 10.2011 | ![GitLab GitLab](logo_gitlab.png) |
ceas | CEAS Cis-regulatory Element Annotation System | 1.0.2 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
centrifuge | Classifier for metagenomic sequences. | 1.0.4_beta | ![GitLab GitLab](logo_gitlab.png) |
charger | Characterization of Germline variants | 0.5.2, 0.5.4 | ![GitLab GitLab](logo_gitlab.png) |
circlator | circlator a tool to circularise genome assemblies | 1.5.5, 1.5.0 | ![GitLab GitLab](logo_gitlab.png) |
clustalo | Latest version of Clustal a multiple sequence alignment program for DNA or proteins | 1.2.4 | ![GitLab GitLab](logo_gitlab.png) |
compilers | A metapackage to obtain compilers | 1.0.4 | ![GitLab GitLab](logo_gitlab.png) |
concoct | Clustering cONtigs with COverage and ComposiTion | 1.1.0, 0.4.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
crossmap | CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies. | 0.3.9 | ![GitLab GitLab](logo_gitlab.png) |
cryolo | Deep learning particle picking procedure based YOLO. | 1.7.4-gpu | ![GitLab GitLab](logo_gitlab.png) |
csvkit | A suite of command-line tools for working with CSV, the king of tabular file formats | 1.0.3 | ![GitLab GitLab](logo_gitlab.png) |
cufflinks | Transcriptome assembly and differential expression analysis for RNA-Seq. | 2.2.1 | ![GitLab GitLab](logo_gitlab.png) |
cutadapt | Trim adapters from high-throughput sequencing reads | 1.8.3, 1.10, 2.10, 1.16, 1.18, 2.3, 2.8 | ![GitLab GitLab](logo_gitlab.png) |
dadi | Fit population genetic models using diffusion approximations to the allele frequency spectrum | 2.0.5 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
delly | Structural variant discovery by integrated paired-end and split-read analysis | 0.7.9, 0.8.1, 0.8.3 | ![GitLab GitLab](logo_gitlab.png) |
diamond | Accelerated BLAST compatible local sequence aligner | 0.9.22, 0.9.28, 0.9.36, 0.9.21 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
discosnp | Designed for discovering all kinds of SNPs | 2.3.0, 2.4.3 | ![GitLab GitLab](logo_gitlab.png) |
dropseq_tools | Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab | 2.3.0 | ![GitLab GitLab](logo_gitlab.png) |
emboss | The European Molecular Biology Open Software Suite | 6.6.0 | ![GitLab GitLab](logo_gitlab.png) |
enabrowsertools | A collection of scripts to assist in the retrieval of data from the ENA Browser | 1.5.4 | ![GitLab GitLab](logo_gitlab.png) |
ensembl-vep | Ensembl Variant Effect Predictor | 98.2 | ![GitLab GitLab](logo_gitlab.png) |
epa-ng | Massively parallel phylogenetic placement of genetic sequences | 0.3.6, 0.2.1, 0.3.5 | ![GitLab GitLab](logo_gitlab.png) |
epic2 | ChIP-seq broad peak calling tool, meant to be easier to use and more performant than SICER | 0.0.41 | ![GitLab GitLab](logo_gitlab.png) |
exonerate | Exonerate - A generic tool for pairwise sequence comparison / alignment | 2.4.0 | ![GitLab GitLab](logo_gitlab.png) |
fastme | | 2.1.5 | ![GitLab GitLab](logo_gitlab.png) |
fastp | A FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...) | 0.20.0, 0.12.5 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
fastqc | A quality control tool for high throughput sequence data. | 0.11.5, 0.11.7, 0.11.8, 0.11.9 | ![GitLab GitLab](logo_gitlab.png) |
fasttree | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences | 2.1.10 | ![GitLab GitLab](logo_gitlab.png) |
fastx_toolkit | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | 0.0.14 | ![GitLab GitLab](logo_gitlab.png) |
filtlong | Filtlong is a tool for filtering long reads by quality | 0.2.0 | ![GitLab GitLab](logo_gitlab.png) |
flye | Fast and accurate de novo assembler for single molecule sequencing reads | 2.6 | ![GitLab GitLab](logo_gitlab.png) |
freebayes | Bayesian haplotype-based polymorphism discovery and genotyping | 1.2.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
gappa | Genesis Applications for Phylogenetic Placement Analysis | 0.5.1, 0.4.0 | ![GitLab GitLab](logo_gitlab.png) |
gatk4 | Genome Analysis Toolkit (GATK4) | 4.0.10.0, 4.1.4.1, 4.1.7.0 | ![GitLab GitLab](logo_gitlab.png) |
gautomatch | Fully automatic acccurate, convenient and extremely fast particle picking for EM | 0.56_sm62_cu8.0 | ![GitLab GitLab](logo_gitlab.png) |
gblocks | Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. | 0.91b | ![GitLab GitLab](logo_gitlab.png) |
gcc | GNU C C++ and Fortran Compiler | 7.3.0, 7.5.0, 8.4.0, 9.3.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
gmap | Genomic mapping and alignment program for mRNA and EST sequences. | 2020.06.01 | ![GitLab GitLab](logo_gitlab.png) |
graphviz | Open Source graph visualization software. | 2.40.1 | ![GitLab GitLab](logo_gitlab.png) |
gridss | GRIDSS a Genomic Rearrangement IDentification Software Suite | 1.9.0 | ![GitLab GitLab](logo_gitlab.png) |
gromacs | GROMACS is a versatile package to perform molecular dynamics. | 2020.2 | ![GitLab GitLab](logo_gitlab.png) |
h5py | Read and write HDF5 files from Python | 2.10.0 | ![GitLab GitLab](logo_gitlab.png) |
hicstuff | General purpose stuff to generate and handle Hi-C data in its simplest form. | 2.3.0 | ![GitLab GitLab](logo_gitlab.png) |
hisat2 | graph-based alignment of next generation sequencing reads to a population of genomes | 2.1.0 | ![GitLab GitLab](logo_gitlab.png) |
hmmer | Biosequence analysis using profile hidden Markov models | 3.2.1 | ![GitLab GitLab](logo_gitlab.png) |
hmmlearn | Hidden Markov Models in Python with scikit-learn like API. | 0.2.4 | ![GitLab GitLab](logo_gitlab.png) |
homer | Software for motif discovery and next generation sequencing analysis | 4.9.1, 4.10, 4.11 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
htslib | C library for high-throughput sequencing data formats. | 1.7, 1.9 | ![GitLab GitLab](logo_gitlab.png) |
humann | HUMAnN The HMP Unified Metabolic Analysis Network, version 3 | 3.0.0.alpha.3 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
isoseq3 | Scalable de novo isoform discovery | 3.3.0 | ![GitLab GitLab](logo_gitlab.png) |
java-jdk | The Zulu OpenJDK build. | 8.0.112 | ![GitLab GitLab](logo_gitlab.png) |
jpredapi | Python library for submitting jobs to JPRED - A Protein Secondary Structure Prediction Server | 1.5.6 | ![GitLab GitLab](logo_gitlab.png) |
kaiju | Fast and sensitive taxonomic classification for metagenomics | 1.7.3 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
keras | Deep Learning for Python | 2.2.4 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
lima | Demultiplex barcoded samples | 1.11.0 | ![GitLab GitLab](logo_gitlab.png) |
links | Long Interval Nucleotide K-mer Scaffolder | 1.8.7 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
lordec | A hybrid error correction program for long, PacBio reads | 0.9 | ![GitLab GitLab](logo_gitlab.png) |
lumpy-sv | a general probabilistic framework for structural variant discovery | 0.3.0 | ![GitLab GitLab](logo_gitlab.png) |
macs2 | Model Based Analysis for ChIP-Seq data | 2.1.1.20160309, 2.2.7.1 | ![GitLab GitLab](logo_gitlab.png) |
mafft | Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform | 7.407, 7.313 | ![GitLab GitLab](logo_gitlab.png) |
maker | MAKER is a portable and easily configurable genome annotation pipeline. | 2.31.10, 2.31.8 | ![GitLab GitLab](logo_gitlab.png) |
manta | Structural variant and indel caller for mapped sequencing data | 1.4.0 | ![GitLab GitLab](logo_gitlab.png) |
mapdamage2 | mapDamage tracking and quantifying damage patterns in ancient DNA sequences http //geogenetics.ku.dk/all_literature/mapdamage/ | 2.0.8 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
mcclintock | Meta-pipeline to identify transposable element insertions using next generation sequencing data | master | ![GitLab GitLab](logo_gitlab.png) |
medaka | Neural network sequence error correction. | 1.0.3 | ![GitLab GitLab](logo_gitlab.png) |
megahit | MEGAHIT An ultra-fast single-node solution for large and complex | 1.2.9, 1.2.8 | ![GitLab GitLab](logo_gitlab.png) |
megan | A tool for studying the taxonomic content of a set of DNA reads | 6.12.3 | ![GitLab GitLab](logo_gitlab.png) |
mercat | Mercat a versatile counter and diversity estimator for data base independent property analysis obtained from whole community sequencing data. | 0.2 | ![GitLab GitLab](logo_gitlab.png) |
metabat2 | Metagenome binning | 2.14 | ![GitLab GitLab](logo_gitlab.png) |
mgltools | MGLTools is an program for visualization and analisys of molecular structures. | 1.5.6 | ![GitLab GitLab](logo_gitlab.png) |
midas | An integrated pipeline for estimating strain-level genomic variation from metagenomic data | 1.3.2, 1.2.2 | ![GitLab GitLab](logo_gitlab.png) |
migrate-n | Population Genetics - Panmixia and Migration detection | 3.6.11, 4.4.4 | ![GitLab GitLab](logo_gitlab.png) |
minimap2 | A versatile pairwise aligner for genomic and spliced nucleotide sequences. | 2.13, 2.17, 2.14 | ![GitLab GitLab](logo_gitlab.png) |
mir-prefer | miR-PREFeR microRNA PREdiction From small RNAseq data | 0.24 | ![GitLab GitLab](logo_gitlab.png) |
mirdeep2 | A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs | 2.0.1.2 | ![GitLab GitLab](logo_gitlab.png) |
mmseqs2 | MMseqs2.0 ultra fast and sensitive sequence search and clustering suite | 8.fac81, 10.6d92c, 11.e1a1c, 8-fac81, 10-6d92c | ![GitLab GitLab](logo_gitlab.png) |
mosdepth | Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing. | 0.2.3, 0.2.6 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
motus | Marker gene-based OTU (mOTU) profiling | 2.5.1 | ![GitLab GitLab](logo_gitlab.png) |
mrbayes | Bayesian Inference of Phylogeny | 3.2.6 | ![GitLab GitLab](logo_gitlab.png) |
msprime | A fast and accurate coalescent simulator. | 0.7.3 | ![GitLab GitLab](logo_gitlab.png) |
multiqc | Create aggregate bioinformatics analysis reports across many samples and tools | 1.6, 1.7, 1.9, 1.3, 1.5 | ![GitLab GitLab](logo_gitlab.png) |
music | MUltiScale enrIchment Calling for ChIP-Seq Datasets | 1.0.0 | ![GitLab GitLab](logo_gitlab.png) |
nanofilt | Filtering and trimming of Oxford Nanopore Sequencing data | 2.7.1 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
nextflow | A DSL for data-driven computational pipelines http //nextflow.io | 18.10.1, 20.04.1, 0.27.6 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
openmpi | An open source Message Passing Interface implementation. | 4.0.4 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
pandoc | Universal markup converter (repackaged binaries) | 2.7.2 | ![GitLab GitLab](logo_gitlab.png) |
parallel | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. | 20190322, 20190722 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
pb-assembly | Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin) | 0.0.2, 0.0.0 | ![GitLab GitLab](logo_gitlab.png) |
pb-falcon | FALCON/Unzip tool-suite (originally by Jason Chin) | 0.2.4 | ![GitLab GitLab](logo_gitlab.png) |
pbcoretools | CLI tools and add-ons for PacBio's core APIs | 0.8.1 | ![GitLab GitLab](logo_gitlab.png) |
pbmm2 | A minimap2 frontend for PacBio native data formats | 1.3.0 | ![GitLab GitLab](logo_gitlab.png) |
pbsv | pbsv - PacBio structural variant (SV) calling and analysis tools | 2.0.2 | ![GitLab GitLab](logo_gitlab.png) |
pdfgrep | A commandline utility to search text in PDF files | 2.1.2 | ![GitLab GitLab](logo_gitlab.png) |
perl-dbd-sqlite | Self Contained RDBMS in a DBI Driver | 1.6.4 | ![GitLab GitLab](logo_gitlab.png) |
perl-vcftools-vcf | cpanm ready distribution of VCFtools Perl libraries | 0.1.16 | ![GitLab GitLab](logo_gitlab.png) |
perl | The Perl programming language interpreter + some libraries
perl-5.26.2 | 5.26.2, 5.26.2 | ![GitLab GitLab](logo_gitlab.png) |
pgdspider | An automated data conversion tool for connecting population genetics and genomics programs | 2.1.1.5 | ![GitLab GitLab](logo_gitlab.png) |
phame | A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes. | 1.0.3 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
phylobayes | PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. | 4.1c | ![GitLab GitLab](logo_gitlab.png) |
phyml | Phylogenetic estimation using (Maximum) Likelihood | 3.3.20180621, 3.3.20190909 | ![GitLab GitLab](logo_gitlab.png) |
picard | Java tools for working with NGS data in the BAM format | 2.10.6, 2.18.9, 2.22.0, 2.23.5 | ![GitLab GitLab](logo_gitlab.png) |
picrust | PICRUSt Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 1.1.3 | ![GitLab GitLab](logo_gitlab.png) |
picrust2 | PICRUSt Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 2.1.1_b | ![GitLab GitLab](logo_gitlab.png) |
pigz | parallel implementation of gzip that exploits multiple processors and multiple cores to the hilt when compressing data | 2.3.4 | ![GitLab GitLab](logo_gitlab.png) |
pilon | Pilon is an automated genome assembly improvement and variant detection tool. | 1.23, 1.22 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
pipmir | PIPmiR algorithm - identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. | 1.1 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
plink2 | Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | 2.00a2.3 | ![GitLab GitLab](logo_gitlab.png) |
porechop | Adapter removal and demultiplexing of Oxford Nanopore reads | 0.2.3_seqan2.1.1 | ![GitLab GitLab](logo_gitlab.png) |
ppanggolin | PPanGGOLiN Depicting microbial species diversity via a Partitioned PanGenome Graph | 1.0.1 | ![GitLab GitLab](logo_gitlab.png) |
prodigal | Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program | 2.6.3 | ![GitLab GitLab](logo_gitlab.png) |
prokka | Rapid annotation of prokaryotic genomes | 1.14.6, 1.13, 1.13.4 | ![GitLab GitLab](logo_gitlab.png) |
psipred | Accurate protein secondary structure prediction | 4.01 | ![GitLab GitLab](logo_gitlab.png) |
pyega3 | EGA python client | 3.0.39 | ![GitLab GitLab](logo_gitlab.png) |
pygtftk | The gtftk suite providing facilities to manipulate genomic annotations in gtf format. | 1.2.2 | ![GitLab GitLab](logo_gitlab.png) |
pypy | PyPy is a Python interpreter and just-in-time compiler. | 2.7-5.10.0, 3.5-7.0.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
qualimap | Quality control of alignment sequencing data and its derivatives like feature counts | 2.2.2b | ![GitLab GitLab](logo_gitlab.png) |
quast | Quality Assessment Tool for Genome Assemblies | 5.0.2 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
raxml-ng | RAxML Next Generation faster, easier-to-use and more flexible | 0.9.0 | ![GitLab GitLab](logo_gitlab.png) |
raxml | Phylogenetics - Randomized Axelerated Maximum Likelihood. | 8.2.12 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
repet | The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale. | 3.0, 2.5 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
roary | Rapid large-scale prokaryote pan genome analysis | 3.12.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
rseqc | RNA-seq QC Package | 2.6.4 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
sambamba | Tools for working with SAM/BAM data | 0.7.1 | ![GitLab GitLab](logo_gitlab.png) |
sample | R is a free software environment for statistical computing and graphics. | 2.13.1, 3.5.1 | ![GitLab GitLab](logo_gitlab.png) |
samtools | Tools for dealing with SAM, BAM and CRAM files | 1.3.1, 1.5, 1.9, 1.10, 1.6 | ![GitLab GitLab](logo_gitlab.png) |
scikit-allel | A Python package for exploring and analysing genetic variation data. | 1.2.1 | ![GitLab GitLab](logo_gitlab.png) |
scikit-learn | Scikit-learn is an open source machine learning library. | 0.22.1 | ![GitLab GitLab](logo_gitlab.png) |
screen | Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells | 4.8.0 | ![GitLab GitLab](logo_gitlab.png) |
seqtk | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format | 1.3 | ![GitLab GitLab](logo_gitlab.png) |
shortstack | ShortStack Comprehensive annotation and quantification of small RNA genes | 3.8.5 | ![GitLab GitLab](logo_gitlab.png) |
sicer | A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
sicer-1.1 | 1.1, 1.1 | ![GitLab GitLab](logo_gitlab.png) |
sickle-trim | Windowed Adaptive Trimming for fastq files using quality | 1.33 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
singularity | | NA | NA ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
sniffles | Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore) | 1.0.10, 1.0.11 | ![GitLab GitLab](logo_gitlab.png) |
snippy | Rapid bacterial SNP calling and core genome alignments | 4.3.3 | ![GitLab GitLab](logo_gitlab.png) |
snpeff | Genetic variant annotation and effect prediction toolbox | 4.3.1t | ![GitLab GitLab](logo_gitlab.png) |
snpsift | Toolbox that allows you to filter and manipulate annotated files | 4.3.1t | ![GitLab GitLab](logo_gitlab.png) |
sortmerna | SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. | 2.1b, 4.2.0 | ![GitLab GitLab](logo_gitlab.png) |
spades | SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. | 3.13.1, 3.14.1 | ![GitLab GitLab](logo_gitlab.png) |
sparcc | SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc). | 0.1.0 | ![GitLab GitLab](logo_gitlab.png) |
sqlite | Implements a self-contained, zero-configuration, SQL database engine | 3.30.1 | ![GitLab GitLab](logo_gitlab.png) |
sra-tools | SRA Toolkit and SDK from NCBI | 2.10.0, 2.10.3 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
star | An RNA-seq read aligner. | 2.6, 2.7.2b, 2.7.5a, 2.7.1a | ![GitLab GitLab](logo_gitlab.png) |
stream | STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http //stream.pinellolab.org | 0.4.1, 1.0, 20180425 | ![GitLab GitLab](logo_gitlab.png) |
stringtie | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | 2.1.2 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
subread | High-performance read alignment, quantification, and mutation discovery | 1.6.1, 2.0.1 | ![GitLab GitLab](logo_gitlab.png) |
swarm | A robust and fast clustering method for amplicon-based studies. | 3.0.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
tetools-l | compute RNA read count for transposable elements and Differential expression analysis of transposable elements | 1.0.0 | ![GitLab GitLab](logo_gitlab.png) |
tetools | Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg | 1.2 | ![GitLab GitLab](logo_gitlab.png) |
texlive | An easy way to get up and running with the TeX document production system | 2019, 20180414 | ![GitLab GitLab](logo_gitlab.png) |
tk | A dynamic programming language with GUI support. Bundles Tcl and Tk. | 8.6.10 | ![GitLab GitLab](logo_gitlab.png) |
tmux | A terminal multiplexer. | 3.1 | ![GitLab GitLab](logo_gitlab.png) |
toil | A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python | 3.14.0 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
tophat | A spliced read mapper for RNA-Seq | 2.1.1 | ![GitLab GitLab](logo_gitlab.png) |
tremolo | Transposable Elements MOvement detection using LOng reads | 0.1 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
trimal | | 1.4.1 | ![GitLab GitLab](logo_gitlab.png) |
trimmomatic | A flexible read trimming tool for Illumina NGS data | 0.36, 0.39 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
ucsc-bedgraphtobigwig | Convert a bedGraph file to bigWig format. | 377 | ![GitLab GitLab](logo_gitlab.png) |
ucsc-bedsort | Sort a .bed file by chrom,chromStart. | 377 | ![GitLab GitLab](logo_gitlab.png) |
ucsc-bigwigtowig | Convert bigWig to wig. This will keep more of the same structure of the | 377 | ![GitLab GitLab](logo_gitlab.png) |
ucsc-fatotwobit | Convert DNA from fasta to 2bit format | 377 | ![GitLab GitLab](logo_gitlab.png) |
umap-learn | Uniform Manifold Approximation and Projection | 0.4.6 | ![GitLab GitLab](logo_gitlab.png) |
umi_tools | Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs) | 1.0.1 | ![GitLab GitLab](logo_gitlab.png) |
unicycler | Hybrid assembly pipeline for bacterial genomes | 0.4.8, 0.4.1, 0.4.3, 0.4.4 | ![GitLab GitLab](logo_gitlab.png) |
varscan | variant detection in massively parallel sequencing data | 2.4.3, 2.4.4 | ![GitLab GitLab](logo_gitlab.png) |
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 | ![GitLab GitLab](logo_gitlab.png) |
velocyto.py | A library for the analysis of RNA velocity. | 0.17.17 | ![GitLab GitLab](logo_gitlab.png) |
virsorter | Mining viral signal from microbial genomic data. | 1.0.6, virsorter | ![GitLab GitLab](logo_gitlab.png) |
vsearch | a versatile open source tool for metagenomics (USEARCH alternative) | 2.14.1, 2.13.1 | ![GitLab GitLab](logo_gitlab.png) |
wtdbg | Wtdbg2 A fuzzy Bruijn graph approach to long noisy reads assembly | 2.5 | ![GitLab GitLab](logo_gitlab.png) |
xgboost | Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for | 0.82 | ![GitLab GitLab](logo_gitlab.png) |
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 | |