Voici la liste des applications installées pour l'Institut Français de Bioinformatique (IFB) sur le Centre de Calcul en tant que modules.
Pour accéder à ces modules, il faut en faire la demande auprès de l'équipe du centre de calcul (via un mail à dnum-cesar-support@unistra.fr par exemple).
IFB SOFTWARES
| Name | Description |
|---|---|
| abricate | "Origin: Conda packages" "Description: Mass screening of contigs for antibiotic resistance genes" |
| admixture | "Origin: Conda packages" "Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets." |
| adxv | adxv can be used to display and analyze 2-D area detector data. It is optimized to display X-Ray crystallography diffraction images. |
| agat | "Origin: Conda packages" "Description: Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." |
| alientrimmer | "Origin: Conda packages" Description: Trimmer of contaminant oligonucleotide sequences such as primers and adapters |
| alphafold | "Origin: Conda packages" "Description: This package provides an implementation of the inference pipeline of AlphaFold v2.0" |
| angsd | "Origin: Conda packages" "Description: ANGSD: Analysis of next generation Sequencing Data" |
| anndata | "Origin: Conda packages" "Description: An annotated data matrix" |
| antismash | "Origin: Conda packages" "Description: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell" |
| anvio | "Origin: Conda packages" Description: An interactive analysis and visualization platform for omics data |
| aria2 | "Origin: Conda packages" "Description: aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink." |
| aspera-cli | "Origin: Singularity image" "Description: IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line." |
| assemblytics | "Origin: Conda packages" Description: analyze a genome assembly by comparing it to a reference genome |
| atlas | "Origin: Singularity image" "Description: ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute." |
| 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. |
| aws-cli | "Origin: Singularity image" "Description: Universal Command Line Interface for Amazon Web Services" |
| axondeepseg | "Origin: Singularity image" "Description: AxonDeepSeg is an open-source software using deep learning and aiming at automatically segmenting axons and myelin sheaths from microscopy images. It performs 3-class semantic segmentation using a convolutional neural network." |
| bam-readcount | "Origin: Conda packages" "Description: Count bases in BAM/CRAM files" |
| bam2fastx | Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files |
| bamscale | "Origin: Conda packages" "Description: BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods." |
| bamtools | "Origin: Conda packages" "Description: C++ API & command-line toolkit for working with BAM data" |
| barrnap | "Origin: Conda packages" "Description: Barrnap predicts the location of ribosomal RNA genes in genomes. (bacteria, archaea, metazoan mitochondria and eukaryotes.)" |
| bbmap | "Origin: Conda packages" "Description: BBMap is a short read aligner, as well as various other bioinformatic tools." |
| 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. |
| beagle-lib | "Origin: Conda packages" "Description: general purpose library for evaluating the likelihood of sequence evolution on trees" |
| beast | "Origin: Conda packages" "Description: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC" |
| beast2 | "Origin: Conda packages" "Description: BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences." |
| bedops | "Origin: Conda packages" "Description: High-performance genomic feature operations." |
| bedtools | A powerful toolset for genome arithmetic |
| bifrost | "Origin: Conda packages" "Description: Highly parallel construction and indexing of colored and compacted de Bruijn graphs" |
| bigscape | "Origin: Conda packages" "Description: Biosynthetic Genes Similarity Clustering and Prospecting Engine." |
| bio-vcf | Smart VCF parser |
| bioawk | "Origin: Conda packages" "Description: BWK awk modified for biological data" |
| bioblend | "Origin: Conda packages" "Description: CloudMan and Galaxy API library" |
| blast | "Origin: Conda packages" "Description: BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit." |
| blast-legacy | "Origin: Conda packages" "Description: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences." |
| blobtools | "Origin: Conda packages" Description: Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets |
| bmge | "Origin: Conda packages" "Description: BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference. " |
| bmtool | "Origin: Conda packages" "Description: bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets" |
| bowtie | "Origin: Conda packages" "Description: An ultrafast memory-efficient short read aligner" |
| bowtie2 | Fast and sensitive read alignment |
| bpp-phyl | "Origin: Conda packages" "Description: Bio++ is a set of C++ libraries for Bioinformatics." |
| bracken | "Origin: Conda packages" "Description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample." |
| braker2 | "Origin: Singularity image" "Description: 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." |
| breseq | "Origin: Conda packages" "Description: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data." |
| busco | "Origin: Conda packages" Description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. |
| bustools | "Origin: Conda packages" Description: bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. |
| bwa-mem2 | "Origin: Conda packages" "Description: The next version of bwa-mem" |
| cafe | "Origin: Conda packages" "Description: Computational Analysis of gene Family Evolution (CAFE)" |
| canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. |
| cd-hit | "Origin: Conda packages" "Description: Clusters and compares protein or nucleotide sequences" |
| cellpose | "Origin: Conda packages" "Description: Cellpose, a generalist algorithm for cell and nucleus segmentation" |
| charger | Characterization of Germline variants |
| checkm-genome | "Origin: Conda packages" "Description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes." |
| checkv | "Origin: Conda packages" "Description: Assess the quality of metagenome-assembled viral genomes." |
| chip-r | "Origin: Conda packages" "Description: ChIP-R is a method for assessing the reproducibility of replicated ChIP-seq or ATAC-seq experiments." |
| circlator | "Origin: Conda packages" "Description: circlator: a tool to circularise genome assemblies" |
| circos | "Origin: Conda packages" "Description: Circos is a software package for visualizing data and information. It visualizes data in a circular layout" |
| clipkit | "Origin: Conda packages" "Description: Alignment trimming software for phylogenetics." |
| clonalframeml | "Origin: Conda packages" "Description: Efficient inferencing of recombination in bacterial genomes" |
| cnv_facets | "Origin: Conda packages" "Description: Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data" |
| compilers | A metapackage to obtain compilers |
| concoct | "Origin: Conda packages" "Description: Clustering cONtigs with COverage and ComposiTion" |
| confindr | "Origin: Conda packages" "Description: Detect intra- and inter-species bacterial contamination in NGS reads" |
| conterminator | "Origin: Conda packages" "Description: Conterminator: software to detect contamination in large sequence sets" |
| coot | "Origin: Singularity image" "Description: Macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data." |
| coreutils | "Origin: Conda packages" "Description: 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." |
| coverm | "Origin: Conda packages" "Description: CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications" |
| cowpy | "Origin: Conda packages" "Description: A cowsay clone for python in one file." |
| cp2k | "Origin: Conda packages" "Description: Quantum chemistry and solid state physics software package" |
| cryolo | Deep learning particle picking procedure based YOLO. |
| cudatoolkit | "Origin: Conda packages" "Description: CUDA Toolkit - Including CUDA runtime" |
| cufflinks | "Origin: Conda packages" "Description: Transcriptome assembly and differential expression analysis for RNA-Seq." |
| culebront | "Origin: Conda packages" "Description: Today, assembly a genome using long reads from Oxford Nanopore Technologies is really interesting in particular to solve repeats and structural variants in prokaryotic as well as in eukaryotic genomes. Assemblies are increasing contiguity and accuracy. The daily increase of data sequences obtained and the fact that more and more tools are being released or updated every week, many species are having their genomes assembled and that’s is great … “But which assembly tool could give the best results for your favorite organism?” CulebrONT can help you! CulebrONT is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch multiple assembly tools in parallel, giving you the possibility of circularise, polish, and correct assemblies, checking quality. CulebrONT can help to choose the best assembly between all possibilities. " |
| curl | "Origin: Conda packages" "Description: tool and library for transferring data with URL syntax" |
| cutadapt | Trim adapters from high-throughput sequencing reads |
| cutesv | "Origin: Conda packages" "Description: cuteSV is a long-read based human genomic structural variation detection tool" |
| dadi | "Origin: Conda packages" "Description: Fit population genetic models using diffusion approximations to the allele frequency spectrum" |
| das_tool | "Origin: Conda packages" "Description: Recovery of genomes from metagenomes via a dereplication," |
| deeparg | "Origin: Conda packages" "Description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deepARG-LS." |
| deeptools | "Origin: Conda packages" Description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data |
| deepvariant | "Origin: Conda packages" "Description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data" |
| delly | Structural variant discovery by integrated paired-end and split-read analysis |
| diamond | Accelerated BLAST compatible local sequence aligner |
| 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 |
| dragmap | "Origin: Conda packages" "Description: Dragmap is the Dragen mapper/aligner Open Source Software." |
| dram | "Origin: Conda packages" "Description: Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes" |
| drep | "Origin: Conda packages" "Description: De-replication of microbial genomes assembled from multiple samples" |
| dropest | "Origin: Singularity image" "Description: Pipeline for initial analysis of droplet-based single-cell RNA-seq data" |
| dsrc | "Origin: Conda packages" "Description: high-performance compression of sequencing reads stored in FASTQ format" |
| eggnog-mapper | "Origin: Conda packages" "Description: Fast genome-wide functional annotation through orthology assignment." |
| eigensoft | "Origin: Conda packages" "Description: The EIGENSOFT package implements methods for analzing population structure and performing stratification correction" |
| elprep | "Origin: Conda packages" "Description: elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." |
| elsa | "Origin: Singularity image" "Description: ELSA - Finding Time-Dependent Associations (Now Augmented with Liquid Associaiton)" |
| ema | "Origin: Conda packages" "Description: Fast & accurate alignment of barcoded short-reads." |
| eman2 | "Origin: Singularity image" "Description: EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes." |
| emblmygff3 | "Origin: Conda packages" "Description: An efficient way to convert gff3 annotation files into EMBL format ready to submit." |
| ena-webin-cli | "Origin: Conda packages" "Description: Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI)." |
| ensembl-vep | "Origin: Conda packages" "Description: Ensembl Variant Effect Predictor" |
| eoulsan | "Origin: Conda packages" "Description: A pipeline and a framework for NGS analysis (RNA-Seq and Chip-Seq)" |
| epa-ng | "Origin: Conda packages" "Description: Massively parallel phylogenetic placement of genetic sequences" |
| ete3 | "Origin: Conda packages" "Description: A Python framework for reconstructing, analysing and visualizing phylogenetic trees and multiple sequence alignments. Includes Python API and Phylogenomic tools" |
| eukrep | "Origin: Conda packages" Description: Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets |
| exonerate | Exonerate - A generic tool for pairwise sequence comparison / alignment |
| fastani | "Origin: Conda packages" "Description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)." |
| fastcat | "Origin: Conda packages" "Description: A set of simply utilities for creating summaries from standard bioinformatics formats." |
| fastlmm | "Origin: Conda packages" "Description: Fast GWAS" |
| fastp | "Origin: Conda packages" "Description: A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)" |
| fastq-pair | "Origin: Conda packages" "Description: fastq-pair: efficient synchronization of paired-end fastq files" |
| 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 |
| fastqc | A quality control tool for high throughput sequence data. |
| faststructure | "Origin: Conda packages" "Description: A variational framework for inferring population structure from SNP genotype data." |
| feelnc | "Origin: Conda packages" "Description: FlExible Extraction of LncRNA" |
| fegenie | "Origin: Conda packages" "Description: HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes." |
| fiji | |
| flanker | "Origin: Conda packages" "Description: Gene-flank analysis tool" |
| flash2 | "Origin: Conda packages" "Description: Merge paired-end reads from fragments that are shorter than twice the read length" |
| flye | "Origin: Conda packages" Description: Fast and accurate de novo assembler for single molecule sequencing reads |
| frogs | "Origin: Conda packages" "Description: FROGS is a workflow designed to metabarcoding sequence analysis" |
| funannotate | "Origin: Conda packages" "Description: funannotate: eukaryotic genome annotation pipeline" |
| fusion-inspector | "Origin: Conda packages" "Description: FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). FusionInspector assists in fusion transcript discovery by performing a supervised analysis of fusion predictions, attempting to recover and re-score evidence for such predictions. - https://github.com/FusionInspector/FusionInspector/wiki" |
| gappa | "Origin: Conda packages" "Description: Genesis Applications for Phylogenetic Placement Analysis" |
| gatk4 | "Origin: Conda packages" "Description: Genome Analysis Toolkit (GATK4)" |
| gautomatch | Fully automatic acccurate, convenient and extremely fast particle picking for EM |
| gcc | "Origin: Conda packages" Description: GNU C C++ and Fortran Compiler |
| genometools-genometools | "Origin: Conda packages" "Description: GenomeTools genome analysis system." |
| genrich | "Origin: Conda packages" "Description: Detecting sites of genomic enrichment." |
| getorganelle | "Origin: Conda packages" "Description: Get organelle genomes from genome skimming data" |
| gffread | "Origin: Conda packages" "Description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more." |
| gffutils | "Origin: Conda packages" "Description: Work with GFF and GTF files in a flexible database framework" |
| git | "Origin: Conda packages" "Description: distributed version control system" |
| git-lfs | "Origin: Conda packages" "Description: An open source Git extension for versioning large files" |
| glimpse | "Origin: Conda packages" "Description: GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." |
| gmap | Genomic mapping and alignment program for mRNA and EST sequences. |
| gmap-fusion | GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly. |
| gmove | "Origin: Singularity image" "Description: gmove - Gene modelling using various evidence." |
| gmx_mmpbsa | "Origin: Conda packages" "Description: gmx_MMPBSA is a tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files." |
| gnuplot | "Origin: Conda packages" "Description: Gnuplot, plotting from command line" |
| gromacs | GROMACS is a versatile package to perform molecular dynamics. |
| gsutil | "Origin: Conda packages" "Description: A command line tool for interacting with cloud storage services." |
| gtdbtk | "Origin: Conda packages" "Description: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." |
| gubbins | "Origin: Conda packages" "Description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins." |
| gunc | "Origin: Conda packages" "Description: Python package for detection of chimerism and contamination in prokaryotic genomes." |
| guppy | "Origin: Singularity image" "Description: Nanopore Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies production basecalling algorithms and several bioinformatic post-processing features" |
| h5py | "Origin: Conda packages" Description: Read and write HDF5 files from Python |
| hapcut2 | "Origin: Conda packages" "Description: Tools for haplotype assembly from sequence data" |
| haslr | "Origin: Conda packages" "Description: A fast tool for hybrid genome assembly of long and short reads" |
| hicexplorer | "Origin: Conda packages" "Description: Set of programs to process, analyze and visualize Hi-C and capture Hi-C data" |
| hicstuff | "Origin: Conda packages" "Description: General purpose stuff to generate and handle Hi-C data in its simplest form." |
| hifiasm | "Origin: Conda packages" "Description: Haplotype-resolved assembler for accurate Hifi reads" |
| hisat2 | "Origin: Conda packages" "Description: Graph-based alignment of next generation sequencing reads to a population of genomes." |
| hmmlearn | "Origin: Conda packages" Description: Hidden Markov Models in Python with scikit-learn like API. |
| homer | "Origin: Conda packages" Description: Software for motif discovery and next generation sequencing analysis |
| htseq | "Origin: Conda packages" "Description: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments." |
| htslib | "Origin: Conda packages" "Description: C library for high-throughput sequencing data formats." |
| humann | HUMAnN: The HMP Unified Metabolic Analysis Network, version 3 |
| idba | "Origin: Conda packages" "Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth." |
| igraph | "Origin: Conda packages" "Description: An open source and free collection of network analysis tool." |
| igv | "Origin: Conda packages" "Description: Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations. " |
| igvtools | "Origin: Conda packages" "Description: command line tools for IGV" |
| ima3 | "Origin: Conda packages" "Description: IMa3 can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange. IMa3 can be used to estimate the rooted phylogenetic tree for multiple populations, and does so while integrating over all possible Isolation-with-Migration models" |
| imagemagick | "Origin: Conda packages" "Description: Software suite to create, edit, compose, or convert bitmap images." |
| imod | "Origin: Singularity image" "Description: IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections." |
| imoka | "Origin: Singularity image" "Description: iMOKA is a software that enables a comprehensive analysis of sequencing data from large cohorts to generate robust classification models or explore specific genetic elements associated with disease etiology." |
| infernal | |
| ipyrad | "Origin: Conda packages" "Description: Interactive assembly and analysis of RAD-seq data sets." |
| iqtree | "Origin: Conda packages" "Description: Efficient software for phylogenomic inference" |
| irep | "Origin: Conda packages" "Description: calculate iRep replication rates from metagenome sequencing" |
| irods | "Origin: Singularity image" "Description: The Integrated Rule-Oriented Data System (iRODS) is open source data management software" |
| ismc | "Origin: Singularity image" "Description: iSMC - The integrated Sequentially Markovian Coalescent" |
| isoquant | "Origin: Conda packages" "Description: IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify transcript models with high precision and decent recall." |
| isoseq3 | "Origin: Conda packages" Description: Scalable de novo isoform discovery |
| java-jdk | "Origin: Conda packages" "Description: The Zulu OpenJDK build." |
| jcvi | "Origin: Singularity image" "Description: Python utility libraries on genome assembly, annotation and comparative genomics" |
| jellyfish | "Origin: Conda packages" "Description: a library for doing approximate and phonetic matching of strings." |
| jq | "Origin: Conda packages" "Description: A command-line JSON processor." |
| julia | "Origin: Singularity image" "Description: The Julia Programming Language" |
| jupyter-book | "Origin: Conda packages" "Description: Create an online book with Jupyter Notebooks" |
| jupyterlab | "Origin: Conda packages" "Description: An extensible environment for interactive and reproducible computing, based on the Jupyter Notebook and Architecture." |
| kaiju | Fast and sensitive taxonomic classification for metagenomics |
| kallisto | "Origin: Conda packages" Description: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. |
| kat | "Origin: Conda packages" "Description: KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts" |
| king | "Origin: Conda packages" "Description: Kinship-based INference for Gwas (KING) is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study <http://people.virginia.edu/~wc9c/KING/>_" |
| kmer-jellyfish | "Origin: Conda packages" "Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence" |
| kodoja | "Origin: Conda packages" "Description: Kodoja: identifying viruses from plant RNA sequencing data" |
| kofamscan | "Origin: Conda packages" "Description: KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam" |
| kraken | "Origin: Conda packages" "Description: Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." |
| kraken2 | Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. |
| krakentools | "Origin: Conda packages" "Description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs." |
| krakenuniq | "Origin: Conda packages" "Description: Metagenomics classifier with unique k-mer counting for more specific results" |
| krona | "Origin: Conda packages" "Description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files." |
| lefse | "Origin: Conda packages" "Description: |
| lima | "Origin: Conda packages" Description: Demultiplex barcoded samples |
| longqc | "Origin: Singularity image" Description: 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. |
| lordec | A hybrid error correction program for long, PacBio reads |
| lra | "Origin: Conda packages" "Description: Long read aligner for sequences and contigs" |
| macs | "Origin: Conda packages" "Description: http://liulab.dfci.harvard.edu/MACS/" |
| macs2 | Model Based Analysis for ChIP-Seq data |
| magicblast | "Origin: Conda packages" "Description: NCBI BLAST next generation read mapper" |
| maker | "Origin: Conda packages" "Description: MAKER is a portable and easily configurable genome annotation pipeline." |
| manta | "Origin: Conda packages" "Description: Structural variant and indel caller for mapped sequencing data" |
| mapdamage2 | "Origin: Conda packages" "Description: mapDamage: tracking and quantifying damage patterns in ancient DNA sequences http://geogenetics.ku.dk/all_literature/mapdamage/" |
| masurca | MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. |
| mauve | "Origin: Conda packages" "Description: Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion" |
| mcclintock | "Origin: Singularity image" Description: Meta-pipeline to identify transposable element insertions using next generation sequencing data |
| medaka | Neural network sequence error correction. |
| megan | "Origin: Conda packages" "Description: A tool for studying the taxonomic content of a set of DNA reads" |
| meme | "Origin: Conda packages" "Description: Motif based sequence Analysis tools" |
| mercat | Mercat: a versatile counter and diversity estimator for data base independent property analysis obtained from whole community sequencing data. |
| merqury | "Origin: Conda packages" "Description: Evaluate genome assemblies with k-mers and more Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose." |
| metabolic | "Origin: Conda packages" "Description: A scalable high-throughput metabolic and biogeochemical functional trait profiler." |
| metawatt | "Origin: Conda packages" "Description: a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning" |
| metawrap | "Origin: Conda packages" "Description: MetaWRAP is a pipeline for genome-resolved metagenomic data analysis" |
| migrate-n | Population Genetics - Panmixia and Migration detection |
| mindthegap | "Origin: Conda packages" "Description: MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap can also be used as a genome assembly finishing tool, it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation." |
| miniasm | "Origin: Conda packages" "Description: Ultrafast de novo assembly for long noisy reads (though having no consensus step)" |
| minimap2 | A versatile pairwise aligner for genomic and spliced nucleotide sequences. |
| minipolish | "Origin: Conda packages" "Description: A tool for Racon polishing of miniasm assemblies" |
| mira | "Origin: Conda packages" "Description: MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)" |
| mitobim | "Origin: Conda packages" "Description: mitochondrial baiting and iterative mapping" |
| mitoz | "Origin: Conda packages" "Description: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes." |
| mmseqs2 | MMseqs2.0: ultra fast and sensitive sequence search and clustering suite |
| moments | "Origin: Conda packages" "Description: Evolutionary inference using SFS and LD statistics." |
| mothur | This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. |
| motus | "Origin: Conda packages" Description: Marker gene-based OTU (mOTU) profiling |
| mrbayes | "Origin: Conda packages" "Description: Bayesian Inference of Phylogeny" |
| msprime | "Origin: Conda packages" "Description: Population genetics simulator" |
| multiqc | Create aggregate bioinformatics analysis reports across many samples and tools |
| mummer4 | "Origin: Conda packages" "Description: MUMmer is a system for rapidly aligning entire genomes" |
| muscle | "Origin: Conda packages" "Description: MUSCLE: multiple sequence alignment with high accuracy and high throughput" |
| mvpart | "Origin: Singularity image" "Description: Multivariate regression trees" |
| mysql-client | "Origin: Conda packages" "Description: MySQL client applications and tools" |
| n2p2 | "Origin: Conda packages" "Description: n2p2 - A Neural Network Potential Package" |
| nanofilt | "Origin: Conda packages" Description: Filtering and trimming of Oxford Nanopore Sequencing data |
| nanopolish | "Origin: Conda packages" "Description: Signal-level algorithms for MinION data" |
| napari | "Origin: Conda packages" "Description: Napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images." |
| ncbi-amrfinderplus | "Origin: Conda packages" "Description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences." |
| 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. |
| netcdf-fortran | "Origin: Conda packages" "Description: Unidata NetCDF Fortran Library" |
| nextclade | "Origin: Conda packages" "Description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks" |
| nextflow | A DSL for data-driven computational pipelines http://nextflow.io |
| nlstradamus | "Origin: Conda packages" "Description: NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction." |
| nonpareil | "Origin: Conda packages" "Description: Estimate average coverage and create curves for metagenomic datasets" |
| opencv | "Origin: Conda packages" "Description: Computer vision and machine learning software library." |
| openjdk | "Origin: Conda packages" "Description: The Zulu OpenJDK build." |
| openmpi | An open source Message Passing Interface implementation. |
| 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. |
| orientagraph | "Origin: Conda packages" "Description: OrientAGraph enables Maximum Likelihood Network Orientation (MNLO), as a standalone routine or as a search heuristic within TreeMix, a popular package for estimating admixture graphs from f-statistics (or related quantities)." |
| orthofinder | "Origin: Conda packages" "Description: Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!" |
| paleomix | "Origin: Conda packages" "Description: The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data" |
| paml | "Origin: Conda packages" "Description: |
| panaroo | "Origin: Conda packages" "Description: panaroo - an updated pipeline for pangenome investigation" |
| pangolearn | "Origin: Conda packages" "Description: Trained model used by Pangolin" |
| pangolin | "Origin: Conda packages" "Description: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments." |
| 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. |
| pbcoretools | "Origin: Conda packages" Description: CLI tools and add-ons for PacBio's core APIs |
| pbmm2 | "Origin: Conda packages" Description: A minimap2 frontend for PacBio native data formats |
| perl | The Perl programming language interpreter + some libraries |
| perl-dbd-sqlite | "Origin: Conda packages" Description: Self Contained RDBMS in a DBI Driver |
| pgdspider | An automated data conversion tool for connecting population genetics and genomics programs |
| pgi | "Origin: Singularity image" "Description: A Comprehensive Suite of Compilers, Libraries and Tools for HPC" |
| phantompeakqualtools | "Origin: Conda packages" Description: 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. |
| phipack | "Origin: Conda packages" "Description: Simple, rapid, and statistically efficient test for recombination." |
| phylip | "Origin: Conda packages" "Description: Package of programs for inferring phylogenies" |
| phylobayes | PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. |
| phylobayes-mpi | "Origin: Conda packages" "Description: A Bayesian software for phylogentic reconstrunction using mixture models" |
| picard | "Origin: Conda packages" Description: Java tools for working with NGS data in the BAM format |
| picrust2 | "Origin: Conda packages" "Description: PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States" |
| pigz | "Origin: Conda packages" Description: parallel implementation of gzip that exploits multiple processors and multiple cores to the hilt when compressing data |
| pixy | "Origin: Conda packages" "Description: pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (AKA monomorphic) sites, which are essential for the correct computation of π and dxy." |
| planemo | "Origin: Conda packages" "Description: Command-line utilities to assist in building tools for the Galaxy project" |
| plink | "Origin: Conda packages" Description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
| plink2 | "Origin: Conda packages" Description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. |
| primer3 | "Origin: Conda packages" "Description: Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it." |
| prodigal | "Origin: Conda packages" Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program |
| prokka | Rapid annotation of prokaryotic genomes |
| pyani | "Origin: Conda packages" "Description: pyani provides a package and script for calculation of genome-scale average nucleotide identity." |
| pygenometracks | "Origin: Conda packages" "Description: Standalone program and library to plot beautiful genome browser tracks." |
| pygtftk | "Origin: Conda packages" Description: The gtftk suite providing facilities to manipulate genomic annotations in gtf format. |
| pyranges | "Origin: Conda packages" "Description: GenomicRanges for Python." |
| pysam | "Origin: Conda packages" "Description: Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix." |
| pyscenic | pySCENIC is 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. |
| pyslim | "Origin: Conda packages" "Description: Tools for dealing with tree sequences coming to and from SLiM.." |
| python | Python is an interpreted, high-level, general-purpose programming language. This env comes with the most common libraries. |
| python-pytorch-tensorflow | "Origin: Conda packages" "Description: Python is an interpreted, high-level, general-purpose programming language. This environment includes most common libraries for data manipulations (Pandas, Numpy), data visualization (Matplotlib, Seaborn, Altair, Plotly ad Bokeh) and machine learning (Tensorflow, PyTorch, Scikit)." |
| pytorch | "Origin: Conda packages" "Description: PyTorch is an optimized tensor library for deep learning using GPUs and CPUs." |
| pyxtermjs | "Origin: Conda packages" "Description: A fully functional terminal in your browser." |
| qdd | "Origin: Singularity image" "Description: QDD - A user-friendly program to select microsatellite markers and design primers from large sequencing projects." |
| qiime2 | "Origin: Conda packages" "Description: QIIME 2™ is a next-generation microbiome bioinformatics platform" |
| quarto | "Origin: Conda packages" "Description: An open-source scientific and technical publishing system built on Pandoc" |
| quast | "Origin: Conda packages" "Description: Quality Assessment Tool for Genome Assemblies" |
| r | R 3.6.3 |
| r-eacon | "Origin: Conda packages" "Description: 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)" |
| r-sartools | "Origin: Conda packages" "Description: Statistical Analysis of RNA-Seq data" |
| r-stitch | "Origin: Conda packages" "Description: STITCH - Sequencing To Imputation Through Constructing Haplotypes" |
| racon | "Origin: Conda packages" "Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads." |
| ragout | "Origin: Conda packages" "Description: Chromosome-level scaffolding using multiple references" |
| ragtag | "Origin: Conda packages" "Description: Fast reference-guided genome assembly scaffolding" |
| rapidnj | "Origin: Conda packages" "Description: RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations." |
| raven-assembler | "Origin: Conda packages" "Description: Raven is an assembler for raw reads generated by the third generation sequencing." |
| raxml-ng | "Origin: Conda packages" "Description: RAxML Next Generation: faster, easier-to-use and more flexible" |
| rdp_classifier | "Origin: Conda packages" "Description: Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus" |
| refinem | "Origin: Conda packages" "Description: A toolbox for improving population genomes." |
| 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) |
| relocate2 | "Origin: Conda packages" "Description: RelocaTE2: a high resolution transposable element insertion sites mapping tool for population resequencing." |
| repeatmasker | "Origin: Conda packages" "Description: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences." |
| repeatmodeler | "Origin: Conda packages" "Description: RepeatModeler is a de-novo repeat family identification and modeling package." |
| repet | "Origin: Singularity image" Description: The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale. |
| rgi | "Origin: Conda packages" "Description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website" |
| rgt | "Origin: Conda packages" "Description: Toolkit to perform regulatory genomics data analysis" |
| rmats | "Origin: Conda packages" "Description: MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data." |
| rnaquast | "Origin: Conda packages" Description: 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. |
| roary | "Origin: Conda packages" "Description: Rapid large-scale prokaryote pan genome analysis" |
| rodeo | "Origin: Conda packages" "Description: RODEO evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs). Because RiPP precursor peptides are small and often evade annotation in sequence databases, RODEO can also manually translate small ORFs (open reading frames). A combination of support vector machine (SVM) learning and motif analysis can be used to scan unannotated intergenic regions for RiPP precursors." |
| rstudio-server | RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server |
| rtg-tools | "Origin: Conda packages" "Description: RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" |
| run-dbcan | "Origin: Conda packages" "Description: Standalone version of dbCAN annotation tool for automated CAZyme annotation" |
| saffontree | "Origin: Conda packages" "Description: SaffronTree: Reference free rapid phylogenetic tree construction from raw read data" |
| saffrontree | "Origin: Conda packages" "Description: SaffronTree: Reference free rapid phylogenetic tree construction from raw read data" |
| saige | "Origin: Singularity image" "Description: SAIGE is an R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N > 400,000)." |
| salmon | "Origin: Conda packages" Description: Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment |
| salsa2 | "Origin: Conda packages" "Description: Salsa is a tool to scaffold long read assemblies with Hi-C." |
| samhaplotag | "Origin: Conda packages" "Description: Processes haplotag barcodes in SAM format." |
| samplot | "Origin: Conda packages" "Description: Plot structural variant signals from BAMs and CRAMs." |
| samtools | Tools for dealing with SAM, BAM and CRAM files |
| sap | "Origin: Singularity image" "Description: SAP makes statistical assingment of an unknown DNA sequence to taxa represented by sequences in GenBank. Each assignment is associated with a posterior probility that serve as a confidence in the assignment." |
| scanpy | "Origin: Conda packages" "Description: Single-Cell Analysis in Python. Scales to >1M cells." |
| screen | Screen is a full-screen window manager that multiplexes a physical terminal between several processes, typically interactive shells |
| seqkit | "Origin: Conda packages" "Description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation" |
| shapeit4 | "Origin: Conda packages" "Description: fast and accurate method for estimation of haplotypes (phasing)" |
| shasta | "Origin: Conda packages" "Description: Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells." |
| sicer | "Origin: Conda packages" Description: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data |
| sicer2 | "Origin: Conda packages" "Description: Redesigned and improved ChIP-seq broad peak calling tool SICER." |
| sift4g | "Origin: Conda packages" "Description: SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms." |
| 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. |
| slim | "Origin: Conda packages" "Description: Forward-time population genetics simulator" |
| smartdenovo | "Origin: Conda packages" "Description: Ultra-fast de novo assembler using long noisy reads" |
| smoove | "Origin: Singularity image" "Description: smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls." |
| snakemake | A popular workflow management system aiming at full in-silico reproducibility. |
| snap-aligner | "Origin: Conda packages" "Description: Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data" |
| sniffles | Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore) |
| soapdenovo2 | "Origin: Conda packages" "Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes." |
| sonicparanoid | "Origin: Conda packages" "Description: SonicParanoid: fast, easy and accurate orthology inference" |
| sortmerna | "Origin: Singularity image" "Description: SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering." |
| spades | "Origin: Conda packages" Description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. |
| spaln | "Origin: Conda packages" "Description: Map and align a set of cDNA/EST or protein sequences onto a genome" |
| squeezemeta | "Origin: Conda packages" "Description: SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins" |
| sra-human-scrubber | "Origin: Conda packages" "Description: An SRA tool identifies and removes any significant human read, and outputs the edited (cleaned) fastq file for SRA submission. |
| sra-tools | "Origin: Conda packages" "Description: SRA Toolkit and SDK from NCBI" |
| srprism | "Origin: Conda packages" "Description: SRPRISM - Short Read Alignment Tool" |
| stacks | "Origin: Conda packages" "Description: Stacks is a software pipeline for building loci from RAD-seq" |
| staden | "Origin: Singularity image" "Description: Staden package - A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin)" |
| star | An RNA-seq read aligner. |
| stream | "Origin: Conda packages" Description: STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data http://stream.pinellolab.org |
| stringtie | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. |
| subread | "Origin: Conda packages" Description: High-performance read alignment, quantification, and mutation discovery |
| swarm | "Origin: Conda packages" "Description: A robust and fast clustering method for amplicon-based studies." |
| tabix | "Origin: Conda packages" "Description: C library and command line tools for high-throughput sequencing data formats." |
| tensorflow | "Origin: Conda packages" "Description: TensorFlow is an open source machine learning framework for everyone." |
| tensorflow-gpu | "Origin: Conda packages" "Description: TensorFlow is an end-to-end open source platform for machine learning." |
| tetools | "Origin: Singularity image" Description: Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg |
| tetools-l | "Origin: Singularity image" Description: compute RNA read count for transposable elements and Differential expression analysis of transposable elements |
| texlive | "Origin: Singularity image" Description: A complete distribution of the Tex/LaTeX document production system |
| tk | "Origin: Conda packages" Description: A dynamic programming language with GUI support. Bundles Tcl and Tk. |
| tmux | A terminal multiplexer. |
| toil | "Origin: Conda packages" "Description: A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python" |
| 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. |
| toulligqc | "Origin: Conda packages" "Description: A post sequencing QC tool for Oxford Nanopore sequencers" |
| transdecoder | "Origin: Conda packages" "Description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks." |
| transrate | "Origin: Conda packages" "Description: Reference free quality assessment of de-novo transcriptome assemblies" |
| treemix | "Origin: Conda packages" "Description: TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations." |
| treeshrink | "Origin: Conda packages" "Description: |
| tremolo | "Origin: Singularity image" Description: Transposable Elements MOvement detection using LOng reads |
| trim-galore | Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control |
| trinity | Trinity assembles transcript sequences from Illumina RNA-Seq data. |
| 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 |
| trust4 | "Origin: Conda packages" "Description: TCR and BCR assembly from bulk or single-cell RNA-seq data" |
| truvari | "Origin: Conda packages" "Description: Structural variant comparison tool for VCFs" |
| trycycler | "Origin: Conda packages" "Description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes" |
| tsinfer | "Origin: Conda packages" "Description: Infer tree sequences" |
| tskit | "Origin: Conda packages" "Description: The tree sequence toolkit." |
| ucsc-bigwigmerge | "Origin: Conda packages" "Description: Merge together multiple bigWigs into a single output bedGraph." |
| ucsc-bigwigtowig | "Origin: Conda packages" Description: Convert bigWig to wig. This will keep more of the same structure of the |
| ucsc-wigtobigwig | "Origin: Conda packages" "Description: Convert ascii format wig file" |
| umap-learn | "Origin: Conda packages" Description: Uniform Manifold Approximation and Projection |
| umi_tools | "Origin: Conda packages" "Description: Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)" |
| unicycler | "Origin: Conda packages" "Description: Hybrid assembly pipeline for bacterial genomes" |
| valet | "Origin: Conda packages" "Description: Pipeline for detecting mis-assemblies in metagenomic assemblies" |
| vamb | "Origin: Conda packages" "Description: Variational autoencoder for metagenomic binning" |
| varscan | variant detection in massively parallel sequencing data |
| vcflib | "Origin: Conda packages" "Description: Command-line tools for manipulating VCF files" |
| velocyto.py | A library for the analysis of RNA velocity. |
| velvet | "Origin: Conda packages" Description: Sequence Assembler for short reads |
| virsorter | "Origin: Conda packages" Description: VirSorter2 -- A multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes |
| vsearch | "Origin: Conda packages" "Description: a versatile open source tool for metagenomics (USEARCH alternative)" |
| vt | "Origin: Conda packages" "Description: A tool set for short variant discovery in genetic sequence data" |
| wiggletools | "Origin: Conda packages" "Description: The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon's rank sum test, etc)." |
| wolfpsort | "Origin: Singularity image" "Description: WoLF PSORT Protein Subcellular Localization Prediction" |
| wtdbg | Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly |
| yacrd | "Origin: Conda packages" "Description: Yet Another Chimeric Read Detector, with long-read mapper result as input." |
| zenodo_get | "Origin: Conda packages" "Description: Zenodo_get - a downloader for Zenodo records" |