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Name Description Links
tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.
A5-miseq is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies.
a simple transcriptome assembler based on kallisto and Cortex graphs.
abismal is a fast and memory-efficient mapper for short bisulfite sequencing reads
an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation.
mass screening of contigs for antibiotic resistance genes.
an abundance-based tool for binning metagenomic sequences.
(Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
(Another Gff Analysis Toolkit) a suite of tools to handle gene annotations in any GTF/GFF format.
Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans).
a python package for annotating gene fusions from the human or mouse genomes.
(Ancestry and Kinship Toolkit) a statistical genetics tool for analysing large cohorts of whole-genome sequenced samples. It provides a handful of useful statistical genetics routines using the htslib API for input/output. This means it can seamlessly read BCF/VCF files and play nicely with bcftools.
is a tool for the efficient processing of single-cell data based on RAD files produced by alevin.
an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.
AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format.
Multi-mapped read rescue strategy for gene regulatory analyses
an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
a modern and open framework for MS-based proteomics.
a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
(Alignment of Multiple Protein Sequences) a suite of programs for protein multiple sequence alignment, pairwise alignment, statistical analysis and flexible pattern matching.
AMPtk: Amplicon tool kit for processing high throughput amplicon sequencing data.
AnchorWave (Anchored Wavefront Alignment) identifies collinear regions via conserved anchors (full-length CDS and full-length exon have been implemented currently) and breaks collinear regions into shorter fragments, i.e., anchor and inter-anchor intervals.
estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
(Advanced Normalization Tools) extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized multimodality image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to …
an open-source, community-driven analysis and visualization platform for ‘omics data. Its interactive interface facilitates the management of metagenomic contigs and associated data for automatic or human-guided identification of genome bins and their curation.
ARAGORN identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf.
high-resolution HLA typing from RNA seq.
Scaffolding genome sequence assemblies using linked or long reads.
(Antibiotic Resistance Identification By Assembly) a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.
a command-line genome browser running from terminal window and solely based on ASCII characters.
Get assembly statistics from FASTA and FASTQ files.
trim adapters from high-throughput sequencing reads.
a gene prediction program for eukaryotes that can be used as an ab initio program, which means it bases its prediction purely on the sequence.
(Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
rapid and standardized annotation of bacterial genomes & plasmids.
A universal protein model for prokaryotic gene prediction
bam2fastx provides conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.
bam-readcount generates metrics at single nucleotide positions.
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.
Extract coverage information from BAM files, supporting stranded and physical coverage and streams.
Tool for converting 10x BAMs produced by Cell Ranger
a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam.
(BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes (bacteria, archaea, metazoan mitochondria and eukaryotes).
is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files. Bazam is a smarter way to realign reads from one genome to another. If you've tried to use Picard SAMtoFASTQ or samtools bam2fq before and ended up unsatisfied with complicated, long running inefficient pipelines, bazam might be what you wanted. Bazam will output FASTQ in a form that can …
a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving.
is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.
provides best-practice pipelines for automated analysis of high throughput sequencing data with the goal of being quantifiable, analyzable, scalable and reproducible. The development process is fully open and sustained by contributors from multiple institutions. Bioinformaticians, biologists and the general public should be able to run these tools on inputs ranging from research materials to clinical samples to personal genomes.
Prioritize small variants, structural variants and coverage based on biological inputs. The goal is to use pre-existing knowledge of relevant genes, domains and pathways involved with a disease to extract the most interesting signal from a set of high quality small or structural variant calls. Given information on coverage, it will be able to identify poorly covered regions in potential genes of interest.
bcbio-variation is a toolkit to analyze genome variation data, built on top of the Genome Analysis Toolkit (GATK) with Clojure. It supports scoring for the Archon Genomics X PRIZE competition and is also a general framework for variant file comparison. It enables validation of variants and exploration of algorithm differences between calling methods by automating the process involved with comparing two sets of variants. …
Parallel merging, squaring off and ensemble calling for genomic variants. Provide a general framework meant to combine multiple variant calls, either from single individuals, batched family calls, or multiple approaches on the same sample. Splits inputs based on shared genomic regions without variants, allowing independent processing of smaller regions with variant calls.
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.
is a software package for phasing genotypes and imputing ungenotyped markers.
is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), sophisticated analyses …
(Binding and Expression Target Analysis) a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data.
is a compact file format for efficiently storing and querying whole-genome genotypes of tens to hundreds of thousands of samples. It can be considered as an alternative to genotype-only BCFv2. BGT is more compact in size, more efficient to process, and more flexible on query.
Brain Imaging Data Structure (BIDS) validator.
A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read GC-content distribution, and base Ns quality. More importantly, BIGpre incorporates associated programs to detect and remove duplicate reads after taking sequencing errors into account and trimming low quality reads from raw data as well.
an extension to Brian Kernighan's awk, with added support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q, and TAB-delimited formats with column names along with new built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk should behave exactly like the original BWK awk.
tools for early stage NGS alignment file processing including fast sorting and duplicate marking.
tools to analyze and comprehend high-throughput genomic data.
Installation Client for the BioGrids software collection.
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Other
subtype microbial whole-genome sequencing (WGS) data using SNV targeting k-mer subtyping schemes.
The bioinfokit toolkit aims to provide various easy-to-use functionalities to analyze, visualize, and interpret the biological data generated from genome-scale omics experiments.
a set of tools for the time-efficient analysis of Bisulfite-Seq (BS-Seq) data. Bismark performs alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls at the same time.
(Basic Local Alignment with Successive Refinement) maps Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error.
(Basic Local Alignment Search Tool) finds regions of similarity between biological sequences.
a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
a 3D creation suite that supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking.
is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. It uses the disk streaming k-mer counting algorithm contained in the GATB library, and inserts solid k-mers in a bloom-filter. The correction procedure is similar to the Musket multistage approach. Bloocoo yields similar results while requiring far less memory: as an example, it can correct whole …
aka Best Match Tagger is for removing human reads from metagenomics datasets
bmtool is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets.
the Amazon Web Services (AWS) SDK for Python, which allows Python developers to write software that makes use of Amazon services like S3 and EC2. Boto provides an easy to use, object-oriented API as well as low-level direct service access.
an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.
an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
implements a versatile high-performance version of the BPP software
(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.
a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs.
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatbility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
Bam and Variant Analysis Tools
(Burrows-Wheeler Aligner) a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
is a command-line tool for converting 3D images between common file formats.
(Concatemeric Consensus Caller with Partial Order alignments) is a computational pipeline for calling consensi on R2C2 nanopore data.
a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs.
clusters paired-end reads using their barcodes and sequences.
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. Canu specializes in assembling PacBio or Oxford Nanopore sequences. Canu operates in three phases: correction, trimming and assembly. The correction phase will improve the accuracy of bases in reads.
a tool for calling copy number variants (CNVs) from human DNA sequencing data.
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
is a Python package designed to make drawing maps for data analysis and visualisation easy.
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Other
Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
clusters and compares protein or nucleotide sequences.
CEFCIG (Computational Epigenetic Framework for Cell Identity Gene Discovery)
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
is a publicly available repository of curated receptors, ligands and their interactions.
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Other
a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.
a set of analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Single Cell ATAC data.
Efficient genotyping bi-allelic SNPs on single cells
an interactive explorer for single-cell transcriptomics data
is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial …
A complete suite for gene-by-gene schema creation and strain identification.
ChIPs is a tool for simulating ChIP-sequencing experiments.
Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.
is an ultrafast method for aligning and preprocessing high throughput chromatin profiles.
a comprehensive and integrative circular RNA analysis toolset.
Circlator is a tool to circularize genome assemblies. The input is a genome assembly in FASTA format and corrected PacBio or nanopore reads in FASTA or FASTQ format. Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.
a software package for visualizing data and information. It visualizes data in a circular layout.
Keywords:
Visualization
count antibody TAGS from a CITE-seq and/or cell hashing experiment.
a tool for symphonizing pileup and full-alignment for high-performance long-read variant calling
fast, accurate and versatile k-mer based classification system.
a general purpose multiple sequence alignment program for DNA or proteins.
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is the latest version of Clustal: a multiple sequence alignment program for DNA or proteins.
a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
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Other
a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
a tool that makes Run VS Code on any machine anywhere and access it in the browser.
an easy-to-use Notebook based environment for fast and convenient protein structure predictions.
Comet MS/MS searches uninterpreted tandem mass spectra of peptides against sequence databases.
uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
Copy number and genotype annotation from whole genome and whole exome sequencing data.
is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
Software for clustering de novo assembled transcripts and counting overlapping reads.
a tool to generate BED coverage tracks from BAM files. It reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range.
Crass is designed to identify and reconstruct CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set.
Bioinformatics tool outputs converter to JSON or YAML.
a tool that enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program with improved specificity and indication on the CRISPR orientation. MacSyFinder is used to identify cas genes, the CRISPR-Cas type and subtype.
a Workflow Management System geared towards scientific workflows.
a program for genome coordinates conversion between different genome assemblies.
controllable lossy compression of BAM/CRAM files.
a set of tools for manipulation of CSV/TSV files. It is convenient for rapid data investigation and integration into analysis pipelines.
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Other
a tool that helps redistributable software libraries to support CUDA applications for Linux.
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Other
a reference-guided assembler that assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from genome reference(s).
a libre server and cloud storage browser for Mac and Windows with support for FTP, SFTP, WebDAV, Amazon S3, OpenStack Swift, Backblaze B2, Microsoft Azure & OneDrive, Google Drive and Dropbox.
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Other
a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.
finds all significant local alignments between reads.
simple de novo transcriptome annotator
a toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing.
a flexible library for parallel computing in Python.
provides joint management of analysis code and data. This enables you to comprehensively track the exact state of any analysis inputs that produced your results — across the entire lifetime of a project, and across multiple datasets.
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Other
GNU datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files.
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Other
is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.
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DCMTK is a collection of libraries and applications implementing large parts the DICOM standard.
dDocent is simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set.
Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles.
Retention time prediction for (modified) peptides using Deep Learning.
a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read and long-read massively parallel sequencing data.
Genetic multiplexing of barcoded single cell RNA-seq.
deconvolutes mixed genomes with unknown proportions.
RNA sequence design for a target protein sequence
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Other
De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
a Bioconductor software package installed in R 3.2.2 that estimates variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
bax file decoder and data compressor.
is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC.
a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
In-silico PCR and variant primer design
is a Python 3.7+ library for very efficient parsing and writing of FASTQ and also FASTA files.
DNAscent is software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform
a set of tools for analyzing DNA methylation data from bisulfite sequencing
a suite of tools for use in genome assembly and consensus.
a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
(Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.
Tools for BED, FASTA, FASTQ, GAF, GFA1/2, GFF3, PAF, SAM, and VCF files
a whole genome simulator for next-generation sequencing based off of wgsim found in SAMtools, which was written by Heng Li, and forked from DNAA. It was modified to handle ABI SOLiD and Ion Torrent data, as well as various assumptions about aligners and positions of indels. Many new features have been subsequently added.
estimates haplotype phase either within a genotyped cohort or using a phased reference panel. Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new, very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas: a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm …
a Bioconductor software package installed in R 3.2.2 for gene and isoform differential expression analysis of RNA-seq data.
a Bioconductor software package installed in R 3.2.2 for examining differential expression of replicated count data.
provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
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Other
Fast genome-wide functional annotation through orthology assignment.
The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).
a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.
Fast & accurate alignment of barcoded short-reads
an extensible, customizable, free/libre text editor.
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Other
a program that integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
EMu is a relative abundance estimator for 16S genomic sequences
a FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files.
predicts the functional effects of genomic variants
a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.
Ultraperformant Chip-Seq broad domain finder based on SICER.
a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
is a software package for Bayesian tree inference.
a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. Starting from a VCF file and a set of phenotypes encoded using the Human Phenotype Ontology (HPO), it will annotate, filter and prioritize likely causative variants based on user-defined criteria such as a variant's predicted pathogenicity, frequency of occurrence in a population and also how closely the given phenotype matches …
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences.
is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
(Fast and Accurate Multiple Sequence Aligner) implements an algorithm for large-scale multiple sequence alignments (400k proteins in 2 hours and 8BG of RAM).
a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!
FastME provides distance algorithms to infer phylogenies.
Fastool is a simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them. It makes use of the KSeq library (http://lh3lh3.users.sourceforge.net/kseq.shtml) for fast access to FastQ/A files.
is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
a quality control tool for high throughput sequence data.
A tool to download FASTQs associated with Study, Experiment, or Run accessions.
fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.
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.
a fast, flexible, user-friendly, cluster-friendly QTL mapper.
infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million sequences in a reasonable amount of time and memory.
an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data.
a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
an application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.
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Other
a set of tools to analyze genomic data with a focus on Next Generation Sequencing.
a CLI tool for interacting with fiberseq bam files.
an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.
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Other
a tool for filtering long reads by quality.
(Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge …
performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data, similar to smartpca from EIGENSOFT (http://www.hsph.harvard.edu/alkes-price/software/) and shellfish (https://github.com/dandavison/shellfish). FlashPCA is based on the https://github.com/yixuan/spectra/ library.
preprocesses high-throughput sequencing data efficiently
fast and accurate de novo assembler for single molecule sequencing reads.
a program that enables fast and sensitive comparisons of large structure sets.
Filter Pairwise Alignment filter long read mapping information to save disk space
is an approximate sequence pattern matcher for FASTQ/FASTA files.
an efficient FASTQ manipulation suite.
Bayesian haplotype-based polymorphism discovery and genotyping.
a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Tool for plotting gene fusion events detected by various tools using Circos.
finds somatic fusion-genes in RNA-seq data.
a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing tools (e.g. lobSTR or hipSTR) is that it can handle repeats that are longer than the read length. GangSTR takes aligned reads (BAM) and a set of repeats in the reference genome as input and outputs a VCF file containing genotypes for each locus.
Genesis Applications for Phylogenetic Placement Analysis
GATE a Monte-Carlo simulation toolkit for medical physics applications
(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
a command-line toolkit that allows biologists to easily build gene co-expression network and predict gene function, especially in RNA-Seq research or lncRNAs annotation
a set of tools and libraries for interacting with Google Cloud products and services.
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Other
(Genome-wide Complex Trait Analysis) a tool for genome-wide complex trait analysis with five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait …
Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP.
a population genetics package that computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including confidence intervals for “neighborhood size”.
Characterizing gene fusions using long transcriptomics reads
a free tool offered by Golden Helix that delivers stunning visualizations of your genomic data, enabling you to see what is occurring at each base pair in your samples.
a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).
Downloads data and metadata from GEO and SRA and creates standard PEPs.
gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.
compares and evaluates the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie), collapses (merges) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples), and classifies transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).
validates, filters, converts and performs various other operations on GFF files (use gffread -h to see the various usage options). Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs. Thus the gffread utility can be used to simply …
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
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is a highly efficient remote homologue detection tool.
a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments.
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
(Globus Command Line Interface) a command line wrapper over the Globus SDK for Python. It is a standalone application that can be installed on the user’s machine and used to access the Globus service.
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Genomic mapping and alignment program for mRNA and EST sequences.
(GNU-based Virus IDentification) a Python3 program for Gene Novelty Unit-based Virus Identification for SARS-CoV-2. It ranks CDS nucleotide sequences in a genome fna file based on the number of observed exact CDS nucleotide matches in a public or private database. It was created to type SARS-CoV-2 genomes using a whole genome multilocus sequence typing (wgMLST) approach.
a set of command line tools to manipulate multiple alignments. Implemented in Go language, Goalign aims to handle multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, through several basic commands. Each command may print result (an alignment, for example) in the standard output, and thus can be piped to the standard input of the next goalign command.
provides functions for working on alignments in fasta format.
memory-efficient de novo assembly of long reads
goleft is a collection of bioinformatics tools written in go distributed together as a single binary.
a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using a declarative query language, in a parallel execution engine. It is very efficient in a wide range of use-cases, including genome wide batch analysis, range-queries, genomic table joins of variants and segments, filtering, aggregation etc.
a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language. The goal is to handle phylogenetic trees in Newick, Nexus and PhyloXML formats, through several basic commands. Each command may print result (a tree for example) in the standard output, and thus can be piped to the standard input of the next gotree command.
grabix leverages the fantastic BGZF library in samtools to provide random access into text files that have been compressed with bgzip. grabix creates it's own index (.gbi) of the bgzipped file. Once indexed, one can extract arbitrary lines from the file with the grab command. Or choose random lines with the, well, random command.
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Sequence to graph aligner for long reads
GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.
GraphMap2 update containins tuning of alignments specific for long RNA reads. GraphMap2 is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.
a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling). It combines variation graph representation of gene sets with an LSH indexing scheme to allow for fast classification of metagenomic reads. Subsequent hierarchical local alignment of classified reads against graph traversals facilitates accurate reconstruction of full-length gene sequences using a simple scoring scheme.
an ultra-fast sequence alignment algorithm for intra-species genome comparison.
is an ultra-fast and scalable microbial genome search program based on MinHash-like metric and graph-based approximate nearest neighbor search
gsMap (genetically informed spatial mapping of cells for complex traits) integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS) summary statistics to map cells to human complex traits, including diseases, in a spatially resolved manner.
a tool to sort genomic files according to a genomefile.
is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees.
a fast browser for genomic sequencing data (.bam/.cram format) used directly from the terminal. GW also allows you to view and annotate variants from vcf/bcf files.
a scalable machine learning and predictive analytics platform.
an open-source, general-purpose, Python-based data analysis library with additional data types and methods for working with genomic data.
Developed for the detection of subtle allelic imbalance events from next-generation sequencing data, hapLOHseq is a sequencing-based extension of hapLOH, which is a method for the detection of subtle allelic imbalance events from SNP array data. It is capable of identifying events of 10 mega-bases or greater occurring in as little as 16% of the sample using exome sequencing data (at 80x) and 4% …
(Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
Automated brain extraction of multi-sequence MRI using artificial neural networks.
Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon.
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s a data model, library, and file format for storing and managing data.
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a bioinformatics tool that helps analyze RNA-seq data, providing base-to-base alignment BAM files, transcript abundance estimation, and fusion gene detection.
an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines.
is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.
A package that can be used to find enriched peak regions from HiChIP datasets that can then be used as an input to available loop calling tools or to do differential peak analysis.
An optimized and flexible pipeline for Hi-C data processing
Blazing fast toolkit to work with .hic and .cool files
A tool for mapping and performing quality control on Hi-C data
Haplotype-resolved assembler for accurate Hifi reads
Metagenome assembler for Hifi reads, based on hifiasm.
HiC alignment and classification pipeline.
(Haplotype inference and phasing for Short Tandem Repeats) a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data. HipSTR was specifically developed to deal with short tandem repeats (STRs) in genomic sequences in the hopes of obtaining more robust STR genotypes.
(Hierarchical Indexing for Spliced Alignment of Transcripts) a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). HISAT2 is a successor to both HISAT and TopHat2.
is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
Hopla enables classic genomic single, duo, trio, etc., analysis, by studying a single (multisample) vcf-file, eventually generating interactive visualizations.
Distributed training framework for TensorFlow, Keras, PyTorch, and Apache MXNet.
is an interactive process viewer.
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a Python package that provides infrastructure to process data from high-throughput sequencing assays.
a C library for reading/writing high-throughput sequencing data.
is a quality control and processing pipeline for High Throughput Sequencing data.
(Histosketching Using Little Kmers) a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
(Hypothesis Testing using Phylogenies) an open-source software package for comparative sequence analysis using stochastic evolutionary models.
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.
(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Creates self-contained html pages for visual variant review with IGV (igv.js).
command line tools for IGV
a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw" and supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.
a software suite to create, edit, compose, or convert bitmap images.
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(IMmunogenetic SEQuence Analysis) is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobolin gene sequencing experiments. It derives immune repertoires from sequencing data in FASTA / FASTQ format.
An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images
(INFERence of RNA ALignment) a program that searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
A sequencing simulator.
efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites.
is a tool for intersection and visualization of multiple genomic region and gene sets (or lists of items).
efficient and versatile phylogenomic software by maximum likelihood.
Scalable De Novo Isoform Discovery
an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble transcripts from RNA-Seq reads (in fasta format). Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting k-mers which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of …
(Insight Toolkit) is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis
is a software application used to segment structures in 3D medical images.
is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
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. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
a small utility to create JSON objects.
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a lightweight and flexible command-line JSON processor.
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a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can: Go from raw fastq files to Hi-C maps binned at many resolutions Automatically annotate loops and contact domains with the Juicer tools Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.
a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
a language-agnostic HTML notebook application for Project Jupyter.
a program for the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.
fast and sensitive taxonomic classification for metagenomics.
a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. Developed with a focus on enabling fast experimentation, Keras is a deep learning library that allows for easy and fast prototyping (through user friendliness, modularity, and extensibility); supports both convolutional networks and recurrent networks, as well as combinations of the two; and runs seamlessly on …
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Kleborate: a tool for typing and screening pathogen genome assemblies
software for RNA-seq investigation using k-mer decomposition
implements a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. KMA is particulary good at aligning high quality reads against highly redundant databases, where unique matches often does not exist. It works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the "ConClave" sorting scheme, and …
KMC—K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. K-mer counting is important for many bioinformatics applications, e.g., developing de Bruijn graph assemblers. Building de Bruijn graphs is a commonly used approach for genome assembly with data from second-generation sequencer. Unfortunately, sequencing errors (frequent in practice) results in huge memory …
accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping
is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments.
a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Metagenomics classifier with unique k-mer counting for more specific results
is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes).
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
Lazy Predict helps build a lot of basic models without much code and helps understand which models works better without any parameter tuning.
Lowest Common Ancestor calculation tool
a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
Leafcutter quantifies RNA splicing variation using short-read RNA-seq data.
Fast and accurate coordinate conversion between assemblies
is a file transfer program that allows sophisticated FTP, HTTP and other connections to other hosts. If site is specified then LFTP will connect to that site otherwise a connection has to be established with the open command.
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is a toolkit to compare genes lifted between genome assemblies.
a kmer-based error correction method for whole genome sequencing data.
is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.
Tools for the structural analysis of RNA
is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.
a computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing
LongReadSum supports FASTA, FASTQ, BAM, FAST5, and sequencing_summary.txt file formats for quick generation of QC data in HTML and text format.
a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).
A long-read analysis toolbox for cancer genomics.
A hybrid error correction program for long, PacBio reads
is a tool for digital spoligotyping of MTB strains from Illumina read data.
Standalone tool and library for working with barcoded linked-reads.
a probabilistic framework for structural variant discovery.
is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.
(Model Based Analysis of ChIP-Seq data) a novel algorithm for identifying transcript factor binding sites.
Model Based Analysis for ChIP-Seq data.
a program to model and detect macromolecular systems, genetic pathways in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features and to allow their efficient detection.
a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
(Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology.
a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. It discovers, assembles, and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. The method is designed for rapid analysis on standard compute hardware: NA12878 at 50x genomic coverage …
An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes.
MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.
a set of fast and accurate sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. This is done by using a reference set of full-length ribosomal RNA sequences for which known taxonomies are known, and for which a set of high quality OTU clusters has been previously generated. For each read, the best guess and corresponding confidence in …
(Mapping and Assembly with Qualities) builds mapping assemblies from short reads generated by the next-generation sequencing machines.
a method for rapid genotype refinement for whole-genome sequencing data using multi-variate normal distribution. Whole-genome low-coverage sequencing has been combined with linkage-disequilibrium (LD) based genotype refinement to accurately and cost-effectively infer genotypes in large cohorts of individuals.
is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads.
A fast approximate aligner for long DNA sequences.
Minimizer based sparse de Bruijn graph constructor.
(Multiple Bacteria Genome Compressor) is a tool for compressing genomes in FASTA (or gzipped FASTA) input format.
an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
a tool to create consensus sequences and variant calls from nanopore sequencing data.
(Manipulation Environment for Genetic Analyses) - data-handling program for facilitating genetic linkage and association analyses.
Megadepth is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files.
an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance.
uses sparse trees to represent gene flow in pedigrees and is a fast pedigree analysis package.
a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.
ATLAS - Three commands to start analysing your metagenome data
The MetaGraph framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data. The indexes can be efficiently queried with any query sequence of interest.
Metagenomic Phylogenetic Analysis
(Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
Metagenomic Pipeline for Short Reads
MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.
MHC I ligand prediction package with competitive accuracy and a fast and documented implementation.
(Metagenomic Inquiry Compressive Acceleration) a family of programs for performing compressively-accelerated metagenomic sequence searches based on BLASTX and DIAMOND.
MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes.
Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to …
a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3.
is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap …
PacBio Minor Variant Calling and Phasing Tools
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).
a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. MISO is installed as a standalone program and as a module within python.
scan contig files against PubMLST typing schemes.
RNA-Seq quantification tool, with special handling on multi-mapping reads.
an ultra fast and sensitive sequence search and clustering suite
(Macromolecular Transmission Format python) is the macromolecular transmission format (MMTF) binary encoding of biological structures.
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.
fast and flexible semi-supervised learning for peptide detection.
a tool that enables quick import and visualisation of structural biology data inside of Blender.
An analysis toolkit for single-cell RNA-seq.
MOODS is a collection of algorithms used to match position weight matrices (PWM) with DNA sequences.
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
a project to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Includes accelerated versions of DOTUR and SONS and the functionality of a number of other popular tools.
marker gene-based OTU (mOTU) profiling.
a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
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a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.
extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
microbiome-related extension to samtools
a tool to integrate a number of Shotgun proteomics tools, generating ready to use result files.
is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
aggregates results from bioinformatics analyses across many samples into a single report.
a versatile alignment tool for DNA and protein sequences.
(multiple sequence comparison by log-expectation) a public domain multiple alignment software for protein and nucleotide sequences.
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collection of utilities for processing Multispecies Whole Genome Alignments
antibiotic resistance prediction in minutes.
Comparing runs of Oxford Nanopore sequencing data and alignments
RNA modification detection using Nanopore raw reads with Deep One Class classification.
Filtering and trimming of long read sequencing data.
a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.
a standard tool to demultiplex Nanopore long read sequencing data.
Plotting tool for long read sequencing data and alignments.
software package for signal-level analysis of Oxford Nanopore sequencing data.
Ultra-fast quality control and summary reports for nanopore reads
Create fastQC-like plots for Oxford Nanopore sequencing data
NanoSim is a fast and scalable read simulator for Nanopore sequencing data.
calculates various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.
a genomic structural variant (SV) caller that utilizes low-depth long-read sequencing such as Oxford Nanopore Technologies (ONT).
Viral genome sequence alignment tool
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
a reactive workflow framework and programming DSL that ease writing computational pipelines with complex data. It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations. Nextflow extends this approach, adding the ability to define complex program interactions and a …
real-time tracking of pathogen evolution.
(NGS Processing with Less Work) enables creation of a pipeline of work for all the first phase of NGS analysis until the point (inclusive) of annotation.
(coNvex Gap-cost alignMents for Long Reads) a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes.
Quick mining and visualization of NGS data by integrating genomic databases
contains programs to perform EM based segmentation of images in nifti or analyse format.
a Python module for fast and easy statistical learning on NeuroImaging data. It leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis.
Nearly Infinite Neighbor Joining Application
the first program capable of inferring variants in a real-time, as read alignments are fed in. Ococo inputs unsorted alignments from a stream and infers single-nucleotide variants, together with a genomic consensus, using statistics stored in compact several-bit counters.
Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time.
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads.
Oncofuse is a framework designed to estimate the oncogenic potential of de-novo discovered gene fusions. It uses several hallmark features and employs a bayesian classifier to provide the probability of a given gene fusion being a driver mutation.
is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format.
(Open Source Computer Vision Library) an open source computer vision and machine learning software library.
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a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.
(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).
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an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.
OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
(Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.
a pipeline for processing and calling high-confidence chromatin loops associated with the ChIPped factor.
a fast, accurate and comprehensive platform for comparative genomics, OrthoFinder is accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!
an Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies.
p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org ) for Unix.
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2D indexing on bgzipped text files of paired genomic coordinates
CLI tools to process mapped Hi-C data
A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
a counting tool for pangenome graphs. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.
a library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. pandas is installed as a module within python.
(Phylogenetic Assignment of Named Global Outbreak LINeages) software package for assigning SARS-CoV-2 genome sequences to global lineages.
a deep-learning based method for predicting splice site strengths.
Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.
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is the world’s leading open source post-processing visualization engine.
is an implementation of the PASTA (Practical Alignment using Saté and TrAnsitivity) algorithm.
pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.
a package that provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
IPA HiFi Genome Assembler
pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in mapped concordance, number of mapped bases, …
PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
PacBio structural variant (SV) calling and analysis tools
Principal Component Analysis All in One
an acronym that standands for Unveil Hi-C Anchors and Peaks, Peakachu takes genome-wide contact data as input and returns coordinates of likely interactions such as chromatin loops.
a tool that takes a set of CLIP-seq peak regions and for each region, individually extracts the most likely site context (transcript or genomic).
compares familial-relationships and sexes as reported in a PED/FAM file with those inferred from a VCF.
a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.
Per-base metrics on BAM/CRAM files.
semi-supervised learning for peptide identification from shotgun proteomics datasets.
Tool to build the parse and the dictionary for VCF files using the approach described in Prefix-Free Parsing for Building Big BWTs
Phantompeakqualtools 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.
a Java-based variant caller designed for detecting somatic deletions from high-coverage (~30x) single-cell whole-genome sequencing (scWGS) data.
(phasing and Allele Specific Expression from RNA-seq) performs haplotype phasing using read alignments in BAM format from both DNA and RNA based assays, and provides measures of haplotypic expression for RNA based assays.
(Phylogenetic Analysis with Space/Time models) a software package for comparative and evolutionary genomics.
PHESANT - PHEnome Scan ANalysis Tool Run a phenome scan (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank. There are three components in this project: Running a phenome scan in UK Biobank Post-processing of results PHESANT-viz: Visualising the results
Prophage finder using multiple metrics
PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
(phy-loo-chee) is a software package that is useful for analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels.
a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
stands for parallel implementation of gzip, and is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
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is the friendly PIL (Python Imaging Library) fork by Alex Clark and Contributors. The Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, an efficient internal representation, and fairly powerful image processing capabilities. The core image library is designed for fast access to data stored in a few basic pixel formats. It should provide a …
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Pilon is a software tool which can be used to automatically improve draft assemblies and find variation among strains, including large event detection.
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. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment.
A commandline tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
is web server for automatically annotating engineered plasmids.
(Protein-Level ASSembler) a software to assemble short read sequencing data on a protein level.
Quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates
Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data.
Plasmid contig classification and characterization for short read draft assemblies.
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been …
a comprehensive update to Shaun Purcell's PLINK command-line program -- a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses.
a tool that infers undirected graphical models to describe coevolution and covariation in families of biological sequences. With a multiple sequence alignment as an input, plmc can quantify inferred coupling strengths between all pairs of positions (couplingsfile output) or infer a generative model of the sequences for predicting the effects of mutations or designing new sequences (paramfile output).
Assembly, consensensus, and analysis tools by ONT research
(Population-wide Deletion Calling) fast structural deletion calling on population-scale short read paired-end germline WGS data.
(POPulation Partitioning Using Nucleotide Kmers) Calculate core and accessory distances, cluster genomes, assign new genomes to clusters, make visualisations
is a suite of population scale analysis tools for single-cell genomics data.
a toolkit for working with nanopore sequencing data from Oxford Nanopore
a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.
predicts the regulatory role of CRP transcription factor in Escherichia coli. PredCRP provides an accurate method for deriving an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites.
a tool aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.
A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
is a fast, reliable protein-coding gene prediction for prokaryotic genomes.
A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes.
a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier.
is a variant caller for single cell data from whole genome amplification with multiple displacement amplification (MDA). It relies on a pair of samples, where one is from an MDA single cell and the other from a bulk sample of the same cell population, sequenced with any next-generation sequencing technology.
a tool to detect orthologous genes within different species.
is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT).
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pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
an interface to the REDCap Application Programming Interface (API), PyCap is designed to be a minimal interface exposing all required and optional API parameters.
a dedicated Python Integrated Development Environment (IDE) providing a wide range of essential tools for Python developers, tightly integrated together to create a convenient environment for productive Python, web, and data science development. The BioGrids-supported version of PyCharm is the open source community edition.
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provides a python wrapper and convenience functions for cudaDeconv, which is a CUDA/C++ implementation of an accelerated Richardson Lucy Deconvolution algorithm1, suitable for general applications, but designed particularly for stage-scanning light sheet applications such as Lattice Light Sheet.
a Python interface to Ensembl reference genome metadata such as exons and transcripts. PyEnsembl downloads GTF and FASTA files from the Ensembl FTP server and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files.
(Python GTF toolkit) a suite providing facilities to manipulate genomic annotations in gtf format.
PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms. Its flexibility and extensibility make it applicable to a large suite of problems.
open source version of the widely used molecular visualization package developed by Warren DeLano.
a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.
a python module that makes it easy to read and manipulate genomic data sets. It is a lightweight wrapper of the htslib C-API; it provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the SAMtools and BCFtools packages. Pysam is installed as a module within python.
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.
a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
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an open source deep learning platform that provides a seamless path from research prototyping to production deployment.
(Unified Complex Network and RecurreNce analysis toolbox) a fully object-oriented Python package for the advanced analysis and modeling of complex networks.
a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.
QTLtools is a tool set for molecular QTL discovery and analysis.
a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
(QUAlity score Reduction at Terabyte scale) an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.
(QUality ASsessment Tool) evaluates genome assemblies by computing various metrics, including N50, length for which the collection of all contigs of that length or longer covers at least 50% of assembly length; NG50, where length of the reference genome is being covered; NA50 and NGA50, where aligned blocks instead of contigs are taken; misassemblies, misassembled and unaligned contigs or contigs bases; and genes and …
an efficient implementation of the Neighbor-Joining algorithm.
compresses next-generation sequencing data with extreme prejudice.
a free software environment for statistical computing and graphics.
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ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
rapid sensitive and accurate read mapping via quasi-mapping.
Randomly subsample sequencing reads to a specified coverage.
a de novo genome assembler for long uncorrected reads.
(Randomized Axelerated Maximum Likelihood) a tool for phylogenetic analysis and post-analysis of large phylogenies.
a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
faster, fully sensitive read mapping.
RBPBench is multi-function tool to evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs.
a command line program to manage files on cloud storage.
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Robust comparative analysis and contamination removal for metagenomics
(reference genome manager) manages storage, access, and transfer of reference genome resources.
is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
is the time-proven, ultra-robust open-source engine for creating complex, data-driven PDF documents and custom vector graphics. It's free, open-source , and written in Python. The package sees 50,000+ downloads per month, is part of standard Linux distributions, is embedded in many products, and was selected to power the print/export feature for Wikipedia.
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a tool for protein hallucination and inpainting with RoseTTAFold.
(Regulatory Genomics Toolbox) is an open source python library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.
a code for performing RING-MaP and PAIR-MaP analysis.
The RNAblueprint library solves the problem of stochastically sampling RNA/DNA sequences compatible to multiple structural constraints.
An open-source tool for rapid analysis of RNA mutational profiling (MaP) experiments.
fast, efficient RNA-Seq metrics for quality control and process optimization.
RNAshape abstraction maps structures to a tree-like domain of shapes.
Takes annotated assemblies in GFF3 format and calculates the pan genome.
(Robust Brain Extraction) is an automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping).
(Rapid ORF Description & Evaluation Online) evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs).
a program that provides an accurate prediction of protein structures and interactions using a 3-track network.
a biomolecular structure prediction neural network that can predict a broad range of biomolecular assemblies.
(RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.
(RNA-seq Quality Control Package) provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
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(RealTimeGenomics Tools) utilities for accurate VCF comparison and manipulation.
a set of ultra fast and robust command line utilities for bioinformatics tasks based on Rust-Bio.
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is a bioinformatics toolkit written in the rust programing language focused around manipulation of alignment (bam and PAF), annotation (bed), and sequence (fasta and fastq) files.
Rustyread, a long-read simulator
Network-Flow based Transcriptome Reconstruction
enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses algorithms to provide very quick, accurate expression estimates using little memory and performs inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.
a high performance, highly parallel, robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Because of its efficiency, it is an important work horse running in many sequencing centres around the world today.
a fast, flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Structural variant (SV) annotation.
a free software that analyzes spatial, temporal and space-time data using the spatial, temporal, or space-time scan statistics. It is designed for any of the following interrelated purposes: Perform geographical surveillance of disease, to detect spatial or space-time disease clusters, and to see if they are statistically significant. Test whether a disease is randomly distributed over space, over time or over space and time. …
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scAllele is a versatile tool to detect and analyze nucleotide variants in scRNA-seq.
Scallop is an accurate reference-based transcript assembler.
reference-based transcriptome assembler for long-reads RNA-seq data
a software package for detecting INDELs.
scCODA is a toolbox for statistical models to analyze changes in compositional data, especially from single-cell RNA-seq experiments.
(single-cell disease-relevance score) is a method for associating individual cells in scRNA-seq data with disease GWASs, built on top of AnnData and Scanpy.
is a single-cell gene expression profile annotation tool using reference datasets.
runs as a two-step process. First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. Second, SCRAMBle-MEIs.R analyzes the cluster file for likely Mobile Element Insertions.
a coalescent simulator for biological sequences.
is a scalable toolkit for RNA velocity analysis in single cells.
(single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.
simple demultiplex tool for FASTQ demultiplexing and dereplication.
Sparse Enrichment Analysis for CUT&RUN
a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing.
a suite of tools for processing of metabolomics data.
a software to map short sequencer reads to reference genomes.
(SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image.
a program to calculate EHH-based scans for positive selection in genomes.
(SATe-enabled Phylogenetic Placement) addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
calculates Per-Read and Total Sequence Complexity from FastQ file.
(Sequece Fastx Utilities) a general-purpose program to manipulate and parse information from FASTA/FASTQ files.
a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.
implements a collapsed haplotype pattern (CHP) method to generate markers from sequence data for linkage analysis.
a Bioconductor software package installed in R 3.2.2 that takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.
an integrated ChIP-seq data interpretation platform.
SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.
a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files, which can also be optionally compressed by gzip.
Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT).
Mapping-free filtering of useless RNA-Seq reads
Short Reads Assembly into Haplotypes (ShoRAH) program for inferring viral haplotypes from NGS data
a windowed adaptive trimming tool for FASTQ files using quality.
simpleaf is a rust framework to make using alevin-fry even simpler.
a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education, interpreted languages.
SINA aligns nucleotide sequences to match a pre-existing MSA using a graph based alignment algorithm similar to PoA. The graph approach allows SINA to incorporate information from many reference sequences building without blurring highly variable regions. While pure NAST implementations depend highly on finding a good match in the reference database, SINA is able to align sequences relatively distant to references with good quality …
SKA2 - Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses.
efficient & high-resolution dereplication of microbial genomes
(Strategic Kmer Extension for Scrupulous Assemblies) a de-novo sequence read assembler for microbial genomes.
implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming. It is specially designed for processing next-generation sequencing (NGS) paired-end sequences.
slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.
is a free and open-source platform for analyzing and understanding medical image data.
an R package that provides functions for inferring continuous, branching lineage structures in low-dimensional data. Designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering, Slingshot is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.
a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.
a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes.
SMALT aligns DNA sequencing reads with a reference genome. Reads from a wide range of sequencing platforms can be processed, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger. Paired reads are supported. There is no support for SOLiD reads.
Local reconstruction of variation graphs using partial order alignment. Pangenome graphs built from raw sets of alignments may have complex local structures generated by common patterns of genome variation. smoothxg can be used to extract the consensus pangenome graph by applying the heaviest bundle algorithm to each chain.
structural variant calling and genotyping with existing tools, but, smoothly.
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
a structural variation caller using third generation sequencing.
Rapid bacterial SNP calling and core genome alignments
converts a FASTA alignment to SNP distance matrix.
genomic variant annotation and functional effect prediction toolbox.
rapidly extracts SNPs from a multi-FASTA alignment.
extracts informative sites, evaluates relatedness, and performs quality-control on BAM/CRAM/BCF/VCF/GVCF.
is an ensemble somatic SNV/indel caller that has the ability to use machine learning to filter out false positives from other callers.
SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering ribosomal RNA from metatranscriptomic data. Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
quickly searches, compares, and analyzes genomic and metagenomic data sets.
(CRISPR Spacer Phage-Host pAiRs findER) a modular toolkit for sensitive phage-host interaction identification using CRISPR spacers.
Visium Spatial Software Suite for analyzing and visualizing spatial gene and protein expression data
(St. Petersburg genome assembler) a genome assembly algorithm designed for single-cell and multi-cell bacterial data sets.
Map and align a set of cDNA/EST or protein sequences onto a genome
a multi-language engine for executing data engineering, data science, and machine learning on single-node machines or clusters.
computational method for finding spa types.
A deep learning-based tool to identify splice variants.

Restriction: SpliceAI models require a license for commercial use. See technical notes for details.
is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.
provides analysis and publication quality printing of linear and circular RNA splicing, expression and regulation.
Software Introduction SPM is made freely available to the [neuro]imaging community, to promote collaboration and a common analysis scheme across laboratories. The software represents the implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package. The SPM software is a suite of MATLAB (MathWorks) functions and subroutines with some externally compiled C routines. SPM was written to organise and interpret …
SIMD partial order alignment tool/library.
is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
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Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure
SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine.
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(Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Mapping small RNA data to a genome.
Short Read Alignment Tool
Haplotyping single-cell DNA sequenced gamete cells.
a software pipeline for building loci from RAD-seq.
(Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Scan genome contigs against the ResFinder and PointFinder databases
Starcode is a DNA sequence clustering software. Starcode clustering is based on all pairs search within a specified Levenshtein distance (allowing insertions and deletions), followed by a clustering algorithm: Message Passing, Spheres or Connected Components. Typically, a file containing a set of DNA sequences is passed as input, jointly with the desired clustering distance and algorihtm. Starcode returns the canonical sequence of the cluster, …
a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT), STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
A tool for bluntifying a bidirected de bruijn graph by removing overlaps.
(Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data.
a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. The germline caller employs an efficient tiered haplotype model to improve accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. The germline caller also analyzes input sequencing data using a mixture-model …
A program to evaluate protein multiple sequence alignments using a single protein structure.
a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that …
a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.
Inference of population structure using multilocus genotype data
comprises a suite of software programs for processing next-gen sequencing read data including

- Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
- Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can …
Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.
a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
Structural variation and indel analysis by assembly.
a computational tool for detecting structural variations from cell free DNA (cfDNA) containing low dilutions of circulating tumor DNA (ctDNA).
a robust and fast clustering method for amplicon-based studies.
(Smith Waterman On Reduced Database) is a fast and sensitive software for protein sequence alignment.
tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
a command-line toolkit for rapid manipulation of NCBI taxonomy data.
profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data.
a software that estimates telomere length from whole genome sequencing data (BAMs).
an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, …
TensorFlow Federated (TFF) is an open-source framework for machine learning and other computations on decentralized data.
enables the discovery of data-driven, robust transcript groups from RNA-seq data.
a system that cleans up raw data files and converts them to pdf format with LaTex. Offers an easy way to get up and running with the TeX document production system.
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A gap-closing software tool that uses error-prone long reads generated by third-generation-sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs to fill N-gap in the genome assembly.
efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain.
Identify and find telomeres, or telomeric repeats in a genome.
is an ncurses-based text-mode interface for git.
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Correct misassemblies using linked or long reads
is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
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a fast distance calculator that computes pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.
(Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal) a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data.
a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
a fast splice junction mapper for RNA-Seq reads that aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
A post sequencing QC tool for Oxford Nanopore sequencers
quantifies mRNA abundance directly from the alignments by parsing BAM files. The input parameters are the same GTF files used to generate the alignments, and one or multiple input BAM file(s) containing either single-end or paired-end sequencing reads. The TPMCalculator output is comprised of four files per sample reporting the TPM values and raw read counts for genes, transcripts, exons and introns respectively.
is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. Tracer v1.7.1 can read output files from MrBayes, BEAST, BEAST2, RevBayes, Migrate, LAMARC and and possibly other MCMC programs from other domains.
tool for fast and accurate white matter bundle segmentation from Diffusion MRI. It can create bundle segmentations, segmentations of the endregions of bundles and Tract Orientation Maps (TOMs). Moreover, it can do tracking on the TOMs creating bundle-specific tractogram and do Tractometry analysis on those.
basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files.
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.
State-of-the-art Natural Language Processing for Jax, Pytorch and TensorFlow
(Tree Building guided by Species Tree) is a versatile program that builds, manipulates and displays phylogenetic trees.
is a phylogenetic penalized likelihood program.
a functional and taxonomic annotation tool for microbial genomes and proteins.
provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.
(Tandem Repeats Finder) a program to locate and display tandem repeats in DNA sequences.
is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
a flexible read trimming tool for Illumina NGS data.
a software package comprised of three independent software modules (Inchworm, Chrysalis, and Butterfly) for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
implements a Bayesian framework for calling de novo mutations in trios for next-generation sequencing data.
tRNA detection in large-scale genome sequence.
Structural variant comparison tool for VCFs
an all-in-one software package for processing and demultiplexing fastq files.
(UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction
tools for processing UMI RNA-tag data.
tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
Fast phylogenetic diversity calculations
toolkit for k-mer with taxonomic information
(UniProt Id Mapping through API) a command line interface for using UniProt's API, which allows access to UniProt's ID mapping programmatically.
a program that rapidly places new samples onto an existing phylogeny using maximum parsimony. It is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny.
is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.
flexible, arbitrary-scenario, uncertainty-aware variant calling with parameter free filtration via FDR control.
a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.

Restriction: available to non-profit users only. See technical notes for additional information on for-profit user licensing.
Convert a vcf in parquet.
allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.
command-line tools for manipulating VCF files.
a program package designed to provide easily accessible methods for working with complex genetic variation data in the form of VCF files, such as those generated by the 1000 Genomes Project.
a library for the analysis of RNA velocity.
a sequence assembler for very short reads.
allows to simultaneously filter variants based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN.
A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
a versatile and efficient RNA-Seq read counting tool
a new tool designed for efficient phylogenetic tree inference, specifically tailored to handle massive taxonomic datasets. It is a highly-tuned implementation based on the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments.
Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: * nodes, which are labeled by sequences and ids * edges, which connect two nodes via either of their respective ends * paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected …
Vienna RNA package -- RNA secondary structure prediction and comparison
a tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins.
a versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements.
an alternative to the USEARCH tool developed by Robert C. Edgar (2010) for which the source code is not publicly available, VSEARCH is an open source, multithreaded 64-bit tool for processing and preparing metagenomics, genomics, and population genomics nucleotide sequence data. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact …
A tool set for short variant discovery in genetic sequence data.
(Visualization Tool Kit) a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
Plotting of aligned sequencing reads, assembled contigs or pan-genome graphs in BAM/CRAM/GFA format and visualization of genomic variants.
WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.
a set of command line tools for sequence logo generation.
a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly.
WhiteMatterAnalysis (WMA) provides fiber clustering and tractography analysis tools.
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).
Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.
a software package for analyzing snapshots of developmental processes in scRNA-seq data.
xAtlas is a fast and retrainable small variant caller that has been developed at the Baylor College of Medicine Human Genome Sequencing Center.
XNAT client tools comprise a number of command line tools to store and retrieve data from XNAT archives. - ArcGet: retrieves image data. - ArcRead: retrieves summary text documents describing imaging data. - ArcSim: retrieves a list of imaging sessions with similar IDs. - StoreXML: writes XML documents to the archive.
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is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing
is a simple and easy to use long read error-correction tool which can detect and remove chimeras.
YaHS, yet another Hi-C scaffolding tool
an extensible parallel framework, written in Python using OpenMPI libraries that allows researchers to quickly build high throughput big data pipelines without extensive knowledge of parallel programming.
discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
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