Awesome Bioinformatics Software

Computational analysis of biological sequences, omics data, and molecular structures.

A curated directory of bioinformatics software organized by research area and analysis task, with package download statistics, GitHub activity, and publication links. Updated regularly.

239 tools | 9 domains | 48 task groups | Downloads: 2026-09 | Repository snapshot: 2026-10-25

• Tools are listed alphabetically within each task group. Stars are GitHub-only and are not a quality score.

• Download counts cover the period shown above. They cannot be compared across sources or added together, and do not represent unique users.

• Updated is the latest commit date.

• - indicates unavailable data.

Contents

• Core & Shared Tools (32)

• Sequence & Genome Analysis (54)

• Genetics & Evolution (23)

• Transcriptomics & Epigenomics (26)

• Microbiome & Metagenomics (33)

• Proteomics & Metabolomics (19)

• Single-cell & Spatial Omics (31)

• Structural Bioinformatics (10)

• Functional Analysis, Integration & Visualization (11)

Core & Shared Tools

Libraries & data access | Sequence & genomic files | Read quality, preprocessing & reports | Sequence alignment, search & clustering | Workflows & platforms

Libraries & data access

Project	Description	Stars	Conda	PyPI	Updated	Paper
Biopython	Official git repository for Biopython (originally converted from CVS)	5,244	273,213	4,030,704	2026-10-22	Bioinformatics (2009)
Biotite	A comprehensive library for computational molecular biology	980	20,146	805,594	2026-10-24	BMC Bioinformatics (2018)
gget	🧬 gget enables efficient querying of genomic reference databases	1,208	176	39,528	2026-10-22	Bioinformatics (2023)
HTSlib	C library for high-throughput sequencing data formats	956	372,543	-	2026-10-22	GigaScience (2021)
pysam	Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF…	911	647,657	1,140,422	2026-09-07	-
scikit-bio	scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and…	1,255	14,879	77,456	2026-10-17	Nat Methods (2026)

See also: Mass spectrometry libraries & formats.

Sequence & genomic files

Project	Description	Stars	Conda	Updated	Paper
bedtools	bedtools - the swiss army knife for genome arithmetic	1,055	171,268	2026-06-10	Bioinformatics (2010)
SAMtools	Tools (written in C using htslib) for manipulating next-generation sequencing data	1,970	323,321	2026-10-22	GigaScience (2021)
SeqKit	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	1,606	50,153	2026-10-19	iMeta (2024)
seqtk	Toolkit for processing sequences in FASTA/Q formats	1,565	29,659	2025-06-01	-

See also: DNA read mapping; RNA-seq alignment & filtering.

Read quality, preprocessing & reports

Project	Description	Stars	Conda	PyPI	Updated	Paper
Cutadapt	Cutadapt removes adapter sequences from sequencing reads	590	30,787	41,254	2026-09-14	EMBnet.journal (2011)
fastp	An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging…)	2,447	48,368	-	2026-10-07	iMeta (2025)
FastQC	A quality control analysis tool for high throughput sequencing data	624	47,060	-	2026-10-07	-
Filtlong	quality filtering tool for long reads	421	1,554	-	2025-09-17	-
MultiQC	Aggregate results from bioinformatics analyses across many samples into a single report.	1,496	33,231	25,601	2026-10-06	Bioinformatics (2016)
NanoPlot	Plotting scripts for long read sequencing data	564	3,727	1,924	2026-09-05	Bioinformatics (2023)

Sequence alignment, search & clustering

Project	Description	Stars	Conda	PyPI	Updated	Paper
BLAST+	-	-	125,166	-	-	BMC Bioinformatics (2009)
CD-HIT	Automatically exported from code.google.com/p/cdhit	732	8,489	-	2021-04-20	Bioinformatics (2012)
DIAMOND	Accelerated BLAST compatible local sequence aligner.	1,331	101,702	-	2026-10-21	Nat Methods (2021)
FAMSA2	Algorithm for ultra-scale multiple protein sequence alignments: 3 million ABC transporters analyzed in 5 minutes and…	277	17,091	-	2026-09-10	Nat Biotechnol (2026)
HH-suite	Remote protein homology detection suite.	630	10,908	-	2026-10-07	BMC Bioinformatics (2019)
HMMER	HMMER: biological sequence analysis using profile HMMs	429	143,635	-	2026-10-24	PLOS Comput Biol (2011)
Kalign	A fast multiple sequence alignment program.	163	2,209	9,378	2026-07-22	Bioinformatics (2020)
MAFFT	Multiple sequence alignment program	-	59,482	-	2025-12-11	Mol Biol Evol (2013)
MMseqs2	MMseqs2: ultra fast and sensitive search and clustering suite	2,158	32,496	-	2026-10-25	Nat Biotechnol (2017)
MUSCLE 5	Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates…	290	45,349	-	2026-08-29	Nat Commun (2022)
T-Coffee	A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence	118	19,998	-	2026-07-21	J Mol Biol (2000)
VSEARCH	Versatile open-source tool for microbiome analysis	762	18,314	-	2026-09-18	PeerJ (2016)

See also: Phylogeny & evolutionary models; Structure search & alignment; Genome & protein annotation.

Workflows & platforms

Project	Description	Stars	Conda	PyPI	Updated	Paper
Galaxy	Data intensive science for everyone.	1,880	-	878	2026-10-25	Nucleic Acids Res (2026)
Nextflow	A workflow language for data-driven computational pipelines	3,517	20,203	-	2026-10-23	Nat Biotechnol (2017)
Rachis	Rachis Framework (Formerly Known as QIIME 2 Framework (Q2F))	533	-	84	2026-10-21	Nat Biotechnol (2019)
Snakemake	This is the development home of the workflow management system Snakemake. For general information, see	2,890	49,629	164,306	2026-10-19	F1000Res (2021)

See also: Integrated microbial analysis; Single-cell analysis & quality; Proteomics processing & DIA.

Sequence & Genome Analysis

DNA read mapping | Genome assembly & assessment | Genome & protein annotation | Resistance, biosynthesis & metabolic models | Comparative genomics | Genome visualization | Variant calling | Variant annotation

DNA read mapping

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
Bowtie 2	A fast and sensitive gapped read aligner	811	214,736	-	-	2026-10-24	Nat Methods (2012)
BWA	Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)	1,769	61,714	-	-	2026-08-07	Bioinformatics (2009)
BWA-MEM2	The next version of bwa-mem	866	15,642	-	-	2025-10-15	IPDPS (2019)
minimap2	A versatile pairwise aligner for genomic and spliced nucleotide sequences	2,259	59,340	57,393	-	2026-05-19	Bioinformatics (2018)
Subread / featureCounts	The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner…	61	16,656	-	8,154	2026-10-24	Bioinformatics (2014)

See also: RNA-seq alignment & filtering; Comparative genomics; Variant calling.

Genome assembly & assessment

Project	Description	Stars	Conda	PyPI	Updated	Paper
ABySS	:microscope: Assemble large genomes using short reads	334	1,026	-	2026-04-30	Genome Res (2017)
BUSCO	Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)	-	12,679	-	2026-06-05	Nucleic Acids Res (2025)
Flye	De novo assembler for single molecule sequencing reads using repeat graphs	954	7,658	-	2025-05-02	Nat Biotechnol (2019)
hifiasm	Hifiasm: a haplotype-resolved assembler for accurate Hifi reads	818	1,979	-	2025-03-18	Nat Methods (2021)
Merqury	k-mer based assembly evaluation	356	978	-	2026-05-21	Genome Biol (2020)
QUAST	Genome assembly evaluation tool	522	6,953	3,692	2026-06-10	Bioinformatics (2013)
SPAdes	SPAdes Genome Assembler	967	26,833	-	2026-10-22	Curr Protoc Bioinformatics (2020)
Unicycler	hybrid assembly pipeline for bacterial genomes	656	2,394	-	2026-07-29	PLOS Comput Biol (2017)
Verkko	Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford…	421	340	-	2026-08-25	Genome Res (2025)

See also: Metagenome assembly & binning; Transcript reconstruction & expression; Microbial genome assessment & taxonomy.

Genome & protein annotation

Project	Description	Stars	Conda	PyPI	Updated	Paper
AUGUSTUS	Genome annotation with AUGUSTUS	346	15,108	-	2026-05-18	Bioinformatics (2008)
Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	686	2,868	362	2026-10-11	Microb Genom (2021)
BRAKER	BRAKER re-implemented with snakemake	469	-	-	2026-09-22	Genome Res (2024)
DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and…	343	-	-	2026-10-19	Nucleic Acids Res (2020)
eggNOG-mapper	Fast genome-wide functional annotation through orthology assignment	798	2,860	788	2026-08-13	Mol Biol Evol (2021)
funannotate	Eukaryotic Genome Annotation Pipeline	402	426	116	2026-10-25	-
InterProScan	Genome-scale protein function classification	393	-	-	2026-10-01	Bioinformatics (2014)
Liftoff	An accurate GFF3/GTF lift over pipeline	562	1,115	301	2023-08-01	Bioinformatics (2021)
PGAP	NCBI Prokaryotic Genome Annotation Pipeline	391	-	-	2026-06-02	Nucleic Acids Res (2016)
Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	237	795	124	2026-08-16	Bioinformatics (2023)
Prodigal	Prodigal Gene Prediction Software	552	37,323	-	2023-01-27	BMC Bioinformatics (2010)
Prokka	:zap: :aquarius: Rapid prokaryotic genome annotation	997	4,393	-	2026-01-06	Bioinformatics (2014)

See also: Resistance, biosynthesis & metabolic models; Viral sequence identification; Gene sets & functional activity.

Resistance, biosynthesis & metabolic models

Project	Description	Stars	Conda	PyPI	Updated	Paper
ABRicate	:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes	515	4,198	-	2026-07-17	-
AMRFinderPlus	AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled…	391	5,520	-	2026-08-10	Sci Rep (2021)
antiSMASH	antiSMASH	270	1,096	-	2026-10-22	Nucleic Acids Res (2025)
CarveMe	CarveMe: genome-scale metabolic model reconstruction	223	138	576	2025-09-12	Nucleic Acids Res (2018)
DeepBGC	BGC Detection and Classification Using Deep Learning	161	183	173	2023-11-11	Nucleic Acids Res (2019)
gapseq	Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks	229	305	-	2026-10-20	Genome Biol (2021)
RGI	Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including…	436	3,480	-	2026-10-17	Nucleic Acids Res (2023)

See also: Genome & protein annotation.

Comparative genomics

Project	Description	Stars	Conda	PyPI	Updated	Paper
FastANI	Fast Whole-Genome Similarity (ANI) Estimation	486	10,742	-	2026-09-14	Nat Commun (2018)
Mash	Fast genome and metagenome distance estimation using MinHash	455	21,570	-	2025-09-19	Genome Biol (2016)
minigraph	Sequence-to-graph mapper and graph generator	492	442	-	2025-08-11	Genome Biol (2020)
minimap2	A versatile pairwise aligner for genomic and spliced nucleotide sequences	2,259	59,340	57,393	2026-05-19	Bioinformatics (2018)
MUMmer4	Mummer alignment tool	578	4,070	-	2025-02-04	PLOS Comput Biol (2018)
OrthoFinder	Phylogenetic orthology inference for comparative genomics	195	2,974	-	2026-10-23	Genome Biol (2019)
Panaroo	An updated pipeline for pangenome investigation	378	1,402	-	2026-07-02	Genome Biol (2020)
PPanGGOLiN	Build a partitioned pangenome graph from microbial genomes	312	1,557	1,120	2026-09-28	PLOS Comput Biol (2020)
skani	Fast average nucleotide identity (ANI) calculator for bacterial genomes, MAGs, and contigs. Supports genome…	269	7,383	-	2026-10-14	Nat Methods (2023)
vg	tools for working with genome variation graphs	1,347	1,288	-	2026-10-25	Nat Biotechnol (2018)

See also: Genome visualization; Microbial genome assessment & taxonomy.

Genome visualization

Project	Description	Stars	Conda	PyPI	Updated	Paper
clinker	Gene cluster comparison figure generator	660	489	1,067	2025-12-18	Bioinformatics (2021)
IGV	Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations	768	1,421	-	2026-10-24	Nat Biotechnol (2011)
JBrowse 2	Source code for JBrowse 2, a modern React-based genome browser	297	1,331	-	2026-10-24	Genome Biol (2023)
pyGenomeViz	A genome visualization python package for comparative genomics	426	310	28,754	2026-06-14	-

See also: Chromatin analysis.

Variant calling

Project	Description	Stars	Conda	PyPI	Updated	Paper
BCFtools	This is the official development repository for BCFtools. See installation instructions and other documentation here…	901	179,828	-	2026-10-24	GigaScience (2021)
Clair3	Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling	394	1,390	-	2026-10-05	Nat Comput Sci (2022)
DeepVariant	DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA…	3,825	369	-	2026-03-19	Nat Biotechnol (2018)
Delly	DELLY2: Structural variant discovery by integrated paired-end and split-read analysis	538	3,157	-	2026-10-14	Bioinformatics (2012)
FreeBayes	Bayesian haplotype-based genetic polymorphism discovery and genotyping.	880	46,291	-	2026-09-03	arXiv (2012)
GATK	Official code repository for GATK versions 4 and up	2,007	15,600	-	2026-08-18	Genome Res (2010)
Sniffles2	Structural variation caller using third generation sequencing	685	2,080	2,593	2026-10-18	Nat Biotechnol (2024)

See also: Association & genetic architecture; Variant annotation.

Variant annotation

Project	Description	Stars	Conda	Updated	Paper
Ensembl VEP	The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants	578	14,442	2026-10-09	Genome Biol (2016)
SnpEff	Genomic variant annotation and functional effect prediction	313	7,381	2026-03-09	Fly (2012)

See also: Variant calling.

Genetics & Evolution

Association & genetic architecture | Population structure, history & simulation | Phylogeny & evolutionary models | Phylogenetic tree analysis & visualization

Association & genetic architecture

Project	Description	Stars	Conda	PyPI	CRAN	Updated	Paper
bigsnpr	R package for the analysis of massive SNP arrays.	227	665	-	2,079	2026-07-10	Bioinformatics (2018)
GCTA	GCTA software	109	-	-	-	2025-07-09	Am J Hum Genet (2011)
GEMMA	Genome-wide Efficient Mixed Model Association	416	558	-	-	2025-12-10	Nat Genet (2012)
LDSC	-	804	-	1,037	-	2026-08-10	Nat Genet (2015)
PLINK	PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic…	529	8,393	16,205	1,100	2026-10-25	GigaScience (2015)
regenie	regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.	271	2,078	-	-	2026-10-02	Nat Genet (2021)
SAIGE	Development for SAIGE and SAIGE-GENE(+)	104	745	-	-	2026-06-26	Nat Genet (2018)
susieR	R package for “sum of single effects” regression.	271	1,403	-	11,057	2026-10-22	J R Stat Soc Series B Stat Methodol (2020)
tensorQTL	Ultrafast GPU-enabled QTL mapper	218	-	8,254	-	2025-06-29	Genome Biol (2019)
TwoSampleMR	R package for performing 2-sample MR using IEU OpenGWAS database	560	-	-	-	2026-10-20	eLife (2018)

See also: Population structure, history & simulation.

Population structure, history & simulation

Project	Description	Stars	Conda	PyPI	Updated	Paper
ADMIXTOOLS 2	-	105	-	-	2026-06-28	eLife (2023)
EIGENSOFT	Eigen tools by Nick Patterson and Alkes Price lab	207	398	-	2026-07-20	PLOS Genet (2006)
msprime	Simulate ARGs and genomic sequence data using population genetic models	218	10,811	22,331	2026-09-15	Genetics (2022)
SLiM	SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology…	235	1,566	-	2026-07-22	Mol Biol Evol (2026)

See also: Association & genetic architecture.

Phylogeny & evolutionary models

Project	Description	Stars	Conda	Updated	Paper
BEAST 2	Bayesian Evolutionary Analysis by Sampling Trees	286	364	2026-03-27	PLOS Comput Biol (2019)
HyPhy 2	HyPhy 2.5.x (Maintenance Mode - bug fixes only). All active development has moved to HyPhy 3…	275	2,550	2026-10-13	Mol Biol Evol (2020)
IQ-TREE	IQ-TREE version 3: software for phylogenetics	338	26,065	2026-09-10	Mol Biol Evol (2026)
MrBayes	MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary…	280	632	2026-10-15	Syst Biol (2012)
PAML	PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please…	209	22,460	2026-01-29	Mol Biol Evol (2007)
RAxML-NG	RAxML Next Generation: faster, easier-to-use and more flexible	-	5,187	2026-09-14	Bioinformatics (2019)

See also: Sequence alignment, search & clustering; Phylogenetic tree analysis & visualization.

Phylogenetic tree analysis & visualization

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
DendroPy	A Python library for phylogenetic scripting, simulation, data processing and manipulation.	237	40,760	88,548	-	2026-10-25	J Open Source Softw (2024)
ETE Toolkit	Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive…	883	5,250	8,468	-	2026-06-01	Mol Biol Evol (2016)
ggtree	:christmas_tree:Visualization and annotation of phylogenetic trees	935	28,118	-	105,250	2026-09-14	Methods Ecol Evol (2017)

Transcriptomics & Epigenomics

RNA-seq alignment & filtering | Transcript reconstruction & expression | Differential expression & splicing | Chromatin analysis | DNA methylation | 3D genome & Hi-C

RNA-seq alignment & filtering

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
HISAT2	Graph-based alignment (Hierarchical Graph FM index)	542	22,691	-	-	2026-07-31	Nat Biotechnol (2019)
minimap2	A versatile pairwise aligner for genomic and spliced nucleotide sequences	2,259	59,340	57,393	-	2026-05-19	Bioinformatics (2018)
SortMeRNA	SortMeRNA: next-generation sequence filtering and alignment tool	303	3,356	-	-	2026-10-24	Bioinformatics (2012)
STAR	RNA-seq aligner	2,273	31,244	-	-	2024-01-25	Bioinformatics (2013)
Subread / featureCounts	The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner…	61	16,656	-	8,154	2026-10-24	Bioinformatics (2014)

See also: Transcript reconstruction & expression; DNA read mapping.

Transcript reconstruction & expression

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
HTSeq	HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS)…	109	70,381	14,275	-	2026-02-04	Bioinformatics (2022)
kallisto	Near-optimal RNA-Seq quantification	775	10,749	-	-	2026-01-20	Nat Biotechnol (2016)
RSEM	RSEM: accurate quantification of gene and isoform expression from RNA-Seq data	479	3,354	-	-	2026-08-03	BMC Bioinformatics (2011)
Salmon	🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment	939	23,843	-	-	2026-09-25	Nat Methods (2017)
SPAdes	SPAdes Genome Assembler	967	26,833	-	-	2026-10-22	Curr Protoc Bioinformatics (2020)
StringTie	Transcript assembly and quantification for RNA-Seq	535	51,687	-	-	2026-06-03	Nat Methods (2026)
Subread / featureCounts	The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner…	61	16,656	-	8,154	2026-10-24	Bioinformatics (2014)
Trinity	Trinity RNA-Seq de novo transcriptome assembly	902	9,685	-	-	2024-08-01	Nat Biotechnol (2011)

See also: RNA-seq alignment & filtering.

Differential expression & splicing

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
DESeq2	Differential expression of RNA-seq data using the Negative Binomial	485	53,807	-	121,204	2026-10-01	Genome Biol (2014)
edgeR	Empirical Analysis of Digital Gene Expression Data in R	-	60,298	-	117,230	2026-10-18	Nucleic Acids Res (2025)
limma	Linear Models for Microarray and Omics Data	-	70,809	-	264,866	2026-10-22	Nucleic Acids Res (2015)
PyDESeq2	A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.	767	4,295	229,277	-	2026-09-28	Bioinformatics (2023)
rMATS turbo	-	312	1,633	-	-	2026-08-10	Nat Protoc (2024)
SUPPA2	SUPPA: Fast quantification of splicing and differential splicing	307	333	149	-	2025-11-06	Genome Biol (2018)

See also: Gene sets & functional activity.

Chromatin analysis

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
ChIPseeker	:dart: ChIP peak Annotation, Comparison and Visualization	259	1,115	-	13,217	2026-10-05	Bioinformatics (2015)
deepTools	Tools to process and analyze deep sequencing data.	770	7,552	7,817	-	2026-10-22	Nucleic Acids Res (2016)
MACS3	MACS – Model-based Analysis of ChIP-Seq	789	2,966	13,555	-	2026-10-21	Genomics Proteomics Bioinformatics (2026)

See also: Single-cell chromatin analysis.

DNA methylation

Project	Description	Stars	Conda	PyPI	Updated	Paper
Bismark	A tool to map bisulfite converted sequence reads and determine cytosine methylation states	468	11,597	-	2026-10-09	Bioinformatics (2011)
MethylDackel	A (mostly) universal methylation extractor for BS-seq experiments.	181	786	-	2026-10-20	-
methylpy	WGBS/NOMe-seq Data Processing & Differential Methylation Analysis	148	94	211	2023-05-20	-
Modkit	A bioinformatics tool for working with modified bases	280	1,808	-	2026-06-12	-

See also: Single-cell chromatin analysis.

3D genome & Hi-C

Project	Description	Stars	Conda	PyPI	Updated	Paper
cooler	A cool place to store your Hi-C	247	6,002	10,051	2026-10-24	Bioinformatics (2020)
HiCExplorer	HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.	281	819	-	2024-11-28	Nucleic Acids Res (2020)
Juicer	A One-Click System for Analyzing Loop-Resolution Hi-C Experiments	492	-	-	2025-08-31	Cell Syst (2016)

Microbiome & Metagenomics

Metagenome assembly & binning | Microbial genome assessment & taxonomy | Microbial classification & abundance | Microbial functional profiling | Amplicons & community analysis | Viral sequence identification | Integrated microbial analysis

Metagenome assembly & binning

Project	Description	Stars	Conda	PyPI	Updated	Paper
CONCOCT	Clustering cONtigs with COverage and ComposiTion	140	932	-	2019-11-11	Nat Methods (2014)
DAS Tool	DAS Tool	178	735	-	2026-10-09	Nat Microbiol (2018)
Flye	De novo assembler for single molecule sequencing reads using repeat graphs	954	7,658	-	2025-05-02	Nat Biotechnol (2019)
MEGAHIT	Ultra-fast and memory-efficient (meta-)genome assembler	727	24,239	-	2025-10-28	Bioinformatics (2015)
MetaBAT 2	MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data	-	-	-	2026-08-20	PeerJ (2019)
SemiBin	SemiBin: metagenomics binning with self-supervised deep learning	175	1,167	381	2026-10-13	Bioinformatics (2023)
SPAdes	SPAdes Genome Assembler	967	26,833	-	2026-10-22	Curr Protoc Bioinformatics (2020)
Vamb	Variational autoencoder for metagenomic binning	335	-	210	2026-04-27	Nat Biotechnol (2021)

See also: Genome assembly & assessment; Microbial genome assessment & taxonomy.

Microbial genome assessment & taxonomy

Project	Description	Stars	Conda	PyPI	Updated	Paper
BUSCO	Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)	-	12,679	-	2026-06-05	Nucleic Acids Res (2025)
CAT/BAT/RAT	CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic…	236	254	-	2026-10-01	Genome Biol (2019)
CheckM	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	411	2,138	722	2026-03-02	Genome Res (2015)
CheckM2	Assessing the quality of metagenome-derived genome bins using machine learning	282	2,458	196	2025-03-20	Nat Methods (2023)
CheckV	Assessing the quality of metagenome-assembled viral genomes	-	1,323	396	2026-05-24	Nat Biotechnol (2021)
dRep	Rapid comparison and dereplication of genomes	360	901	412	2026-10-09	ISME J (2017)
GTDB-Tk	GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.	625	2,186	510	2026-10-13	Bioinformatics (2022)
GUNC	Python package for detection of chimerism and contamination in prokaryotic genomes.	97	483	74	2026-05-11	Genome Biol (2021)

See also: Genome assembly & assessment; Microbial classification & abundance; Comparative genomics; Genome & protein annotation; Viral sequence identification.

Microbial classification & abundance

Project	Description	Stars	Conda	PyPI	Updated	Paper
Bracken	Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the…	358	4,157	-	2026-03-16	PeerJ Comput Sci (2017)
CAT/BAT/RAT	CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic…	236	254	-	2026-10-01	Genome Biol (2019)
CoverM	Read alignment statistics for metagenomics	410	1,300	-	2026-10-20	Bioinformatics (2025)
inStrain	Bioinformatics program inStrain	192	341	120	2026-10-20	Nat Biotechnol (2021)
Kraken 2	The second version of the Kraken taxonomic sequence classification system	948	13,237	-	2026-10-20	Genome Biol (2019)
Metabuli	Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.	186	269	-	2026-10-18	Nat Methods (2024)
MetaPhlAn	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun…	429	2,858	1,071	2026-08-05	Nat Biotechnol (2023)
sylph	ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.	332	1,228	-	2026-10-10	Nat Biotechnol (2025)

See also: Microbial genome assessment & taxonomy.

Microbial functional profiling

Project	Description	Stars	Conda	PyPI	Updated	Paper
HUMAnN	HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).	253	707	1,988	2026-07-10	eLife (2021)
PICRUSt2	Code, unit tests, and tutorials for running PICRUSt2	399	1,199	-	2026-10-23	Nat Biotechnol (2020)

Amplicons & community analysis

Project	Description	Stars	Conda	Bioconductor	CRAN	Updated	Paper
ANCOMBC	Differential abundance (DA) and correlation analyses for microbial absolute abundance data	144	4,016	9,802	-	2026-09-18	Nat Methods (2024)
DADA2	Accurate sample inference from amplicon data with single nucleotide resolution	560	6,402	12,643	-	2026-07-31	Nat Methods (2016)
decontam	Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data	175	4,409	8,492	-	2025-09-04	Microbiome (2018)
MaAsLin	MaAsLin3: Microbiome Multivariate Association with Linear Models	155	425	6,108	-	2026-10-19	Nat Methods (2026)
mothur	Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department…	279	7,408	-	-	2026-08-21	Appl Environ Microbiol (2009)
phyloseq	phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic…	651	6,823	19,992	-	2026-02-27	PLOS One (2013)
vegan	R package for community ecologists: popular ordination methods, ecological null models & diversity analysis	550	96,753	-	145,607	2026-10-23	-

See also: Sequence alignment, search & clustering; Gene sets & functional activity.

Viral sequence identification

Project	Description	Stars	Conda	PyPI	Updated	Paper
geNomad	geNomad: Identification of mobile genetic elements	337	1,695	1,063	2026-10-14	Nat Biotechnol (2024)
VirSorter2	customizable pipeline to identify viral sequences from (meta)genomic data	300	403	-	2024-11-28	Microbiome (2021)

See also: Genome & protein annotation.

Integrated microbial analysis

Project	Description	Stars	Conda	Updated	Paper
anvi’o	An analysis and visualization platform for ‘omics data	544	-	2026-10-22	Nat Microbiol (2021)
Metagenome-Atlas	ATLAS - Three commands to start analyzing your metagenome data	404	303	2025-03-19	BMC Bioinformatics (2020)

Proteomics & Metabolomics

Mass spectrometry libraries & formats | Proteomics processing & DIA | Peptide identification & validation | Metabolomics processing & identification

Mass spectrometry libraries & formats

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
MSnbase	Base Classes and Functions for Mass Spectrometry and Proteomics	140	1,150	-	18,257	2026-10-05	Bioinformatics (2012)
ProteoWizard	The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and…	324	421	-	-	2026-10-24	Bioinformatics (2008)
Pyteomics	Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics…	162	3,985	279,861	-	2026-10-23	J Proteome Res (2019)

See also: Proteomics processing & DIA; Metabolomics processing & identification.

Proteomics processing & DIA

Project	Description	Stars	Conda	PyPI	Updated	Paper
alphaDIA	modular & open DIA search	118	-	201	2026-10-23	Nat Biotechnol (2026)
AlphaPept	A modular, python-based framework for mass spectrometry. Powered by nbdev.	192	-	158	2024-04-19	Nat Commun (2024)
DIA-NN	DIA-NN - a universal automated software suite for DIA proteomics data analysis.	493	-	-	2026-09-16	Nat Methods (2020)
FragPipe	A cross-platform proteomics data analysis suite	327	124	-	2026-08-05	Nat Methods (2017)
OpenMS	The codebase of the OpenMS project	627	917	169,402	2026-10-24	Nat Methods (2024)

See also: Peptide identification & validation.

Peptide identification & validation

Project	Description	Stars	Conda	PyPI	Updated	Paper
AlphaPeptDeep	Deep learning framework for proteomics	160	-	1,131	2026-07-30	Nat Commun (2022)
Casanovo	De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model	204	-	816	2026-10-11	Nat Commun (2024)
Comet	An tandem mass spectrometry (MS/MS) sequence database search tool.	56	7,687	-	2026-10-15	Proteomics (2013)
FragPipe	A cross-platform proteomics data analysis suite	327	124	-	2026-08-05	Nat Methods (2017)
Percolator	Semi-supervised learning for peptide identification from shotgun proteomics datasets	143	667	-	2026-05-21	Nat Methods (2007)
Sage	Proteomics search & quantification so fast that it feels like magic	317	2,366	-	2026-10-22	J Proteome Res (2023)

See also: Proteomics processing & DIA.

Metabolomics processing & identification

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
matchms	Python library for processing (tandem) mass spectrometry data and for computing spectral similarities.	276	1,070	23,080	-	2026-10-08	J Open Source Softw (2020)
MS-DIAL	Universal workbench incorporating msdial, msfinder, and mrmprobs	124	-	-	-	2026-10-22	Nat Methods (2015)
mzmine	mzmine source code repository	307	42	-	-	2026-10-19	Nat Biotechnol (2023)
peakonly	-	122	-	-	-	2021-09-17	Anal Chem (2020)
SIRIUS	SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass…	172	1,509	-	-	2026-08-25	Nat Methods (2019)
xcms	This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis	236	831	-	13,007	2026-10-08	Anal Chem (2025)

See also: Multi-omics integration.

Single-cell & Spatial Omics

Single-cell analysis & quality | Integration, reference mapping & annotation | Cell trajectories, markers & regulation | Cell-cell communication | Single-cell chromatin analysis | Spatial omics analysis & data | Spatial mapping & deconvolution

Single-cell analysis & quality

Project	Description	Stars	Conda	PyPI	CRAN	Updated	Paper
alevin-fry	🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on…	219	1,010	-	-	2026-09-13	Nat Methods (2022)
Cell Ranger	10x Genomics Single Cell Analysis	482	-	-	-	2026-07-16	Nat Commun (2017)
CellBender	CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing…	426	70	3,066	-	2026-08-18	Nat Methods (2023)
DoubletFinder	R package for detecting doublets in single-cell RNA sequencing data	574	157	-	-	2025-03-21	Cell Syst (2019)
Scanpy	Single-cell analysis in Python. Scales to >100M cells.	2,594	30,987	702,628	-	2026-10-23	Genome Biol (2018)
Scrublet	Detect doublets in single-cell RNA-seq data	184	2,515	62,762	-	2020-12-29	Cell Syst (2019)
Seurat	R toolkit for single cell genomics	2,807	24,657	-	58,046	2026-10-23	Nat Biotechnol (2024)
SoupX	R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data	347	1,015	-	3,713	2022-11-01	GigaScience (2020)

See also: Omics visualization & exploration; Integration, reference mapping & annotation; Cell trajectories, markers & regulation.

Integration, reference mapping & annotation

Project	Description	Stars	Conda	PyPI	CRAN	Updated	Paper
CellTypist	A tool for semi-automatic cell type classification	515	2,227	14,331	-	2025-06-25	Science (2022)
Harmony 2	Fast, sensitive and accurate integration of single-cell data with Harmony	676	3,810	-	19,244	2026-10-15	Nat Methods (2019)
muon	muon is a multimodal omics Python framework	279	2,518	14,135	-	2026-10-19	Genome Biol (2022)
Scanorama	Panoramic stitching of single cell data	295	2,724	4,310	-	2025-07-14	Nat Biotechnol (2019)
scArches	Reference mapping for single-cell genomics	414	48	677	-	2026-06-26	Nat Biotechnol (2022)
scvi-tools	Deep probabilistic analysis of single-cell and spatial omics data	1,717	4,068	45,191	-	2026-10-22	Nat Biotechnol (2022)
Seurat	R toolkit for single cell genomics	2,807	24,657	-	58,046	2026-10-23	Nat Biotechnol (2024)

See also: Multi-omics integration; Single-cell chromatin analysis.

Cell trajectories, markers & regulation

Project	Description	Stars	Conda	PyPI	CRAN	Updated	Paper
CellRank	CellRank: dynamics from multi-view single-cell data	459	579	3,784	-	2026-10-14	Nat Methods (2024)
Monocle 3	-	468	1,024	-	-	2026-05-04	Nature (2019)
Presto	Fast Wilcoxon and auROC	220	807	-	238	2026-09-20	bioRxiv (2019)
pySCENIC	pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference…	646	412	4,466	-	2025-01-09	Nat Protoc (2020)
scVelo	RNA Velocity generalized through dynamical modeling	513	1,133	7,254	-	2026-02-25	Nat Biotechnol (2020)
VISION	Signature Analysis and Visualization for Single-Cell RNA-seq	186	67	-	-	2024-06-10	Nat Commun (2019)

Cell-cell communication

Project	Description	Stars	Downloads	Updated	Paper
CellChat	R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially…	790	-	2026-03-04	Nat Protoc (2025)

See also: Cell trajectories, markers & regulation; Spatial omics analysis & data.

Single-cell chromatin analysis

Project	Description	Stars	Conda	PyPI	CRAN	Updated	Paper
ArchR	ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)	467	180	-	-	2025-02-18	Nat Genet (2021)
EpiScanpy	Episcanpy: Epigenomics Single Cell Analysis in Python	153	34	572	-	2024-12-05	Nat Commun (2021)
Signac	R toolkit for the analysis of single-cell chromatin data	431	1,550	-	6,036	2026-04-06	Nat Methods (2021)
SnapATAC2	Single-cell epigenomics analysis tools	329	766	4,929	-	2026-08-14	Nat Methods (2024)

See also: Chromatin analysis; DNA methylation.

Spatial omics analysis & data

Project	Description	Stars	Conda	PyPI	Updated	Paper
Giotto Suite	Spatial omics analysis toolbox	394	-	-	2026-08-26	Genome Biol (2021)
SpatialData	An open and interoperable data framework for spatial omics data	403	3,761	89,013	2026-10-21	Nat Methods (2025)
Squidpy	Spatial Single Cell Analysis in Python	611	3,128	66,635	2026-10-09	Nat Methods (2022)

See also: Spatial mapping & deconvolution.

Spatial mapping & deconvolution

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
cell2location	Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics…	463	-	2,250	-	2026-02-22	Nat Biotechnol (2022)
spacexr / RCTD	Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential…	489	36	-	3,613	2026-01-22	Nat Biotechnol (2022)
Tangram	Spatial alignment of single cell transcriptomic data.	375	-	1,160	-	2025-07-01	Nat Methods (2021)

Structural Bioinformatics

Structure prediction & protein design | Structure search & alignment | Molecular visualization

Structure prediction & protein design

Project	Description	Stars	Conda	PyPI	Updated	Paper
AlphaFold 2	Open source code for AlphaFold 2.	14,910	-	-	2026-04-22	Nature (2021)
AlphaFold 3	AlphaFold 3 inference pipeline.	8,678	-	-	2026-10-23	Nature (2024)
Boltz	Official repository for the Boltz biomolecular interaction models	4,269	-	19,925	2026-05-29	bioRxiv (2025)
ColabFold	Making Protein folding accessible to all!	2,970	207	7,519	2026-10-21	Nat Methods (2022)
ProteinMPNN	Code for the ProteinMPNN paper	1,890	-	-	2023-06-27	Science (2022)
RFdiffusion	Code for running RFdiffusion	3,106	-	-	2026-07-15	Nature (2023)

See also: Structure search & alignment; Molecular visualization.

Structure search & alignment

Project	Description	Stars	Conda	Updated	Paper
Foldseek	Foldseek enables fast and sensitive comparisons of large structure sets.	1,317	33,175	2026-09-09	Nat Biotechnol (2024)
US-align	Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins	193	3,951	2026-10-19	Nat Methods (2022)

Molecular visualization

Project	Description	Stars	Conda	Updated	Paper
Mol*	A comprehensive macromolecular library	1,036	-	2026-10-25	Nucleic Acids Res (2021)
Open-Source PyMOL	Open-source foundation of the user-sponsored PyMOL molecular visualization system.	1,764	26,714	2026-10-07	-

Functional Analysis, Integration & Visualization

Gene sets & functional activity | Multi-omics integration | Biological networks | Omics visualization & exploration

Gene sets & functional activity

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
clusterProfiler	:bar_chart: A universal enrichment tool for interpreting omics data	1,243	23,638	-	75,674	2026-10-23	Innovation (2021)
decoupler	Python package to perform enrichment analysis from omics data.	300	2,041	29,569	-	2026-10-24	Bioinform Adv (2022)
fgsea	Fast Gene Set Enrichment Analysis	460	31,526	-	67,351	2026-09-22	bioRxiv (2021)
GSEApy	Gene Set Enrichment Analysis in Python	716	6,247	171,320	-	2026-09-02	Bioinformatics (2023)

See also: Genome & protein annotation; Cell trajectories, markers & regulation.

Multi-omics integration

Project	Description	Stars	Conda	PyPI	Bioconductor	Updated	Paper
mixOmics	Development repository for the Bioconductor package ‘mixOmics ‘	270	455	-	12,560	2026-10-23	PLOS Comput Biol (2017)
MOFA2	Multi-Omics Factor Analysis	429	277	8,001	7,099	2026-08-26	Genome Biol (2020)

See also: Integration, reference mapping & annotation; Omics visualization & exploration.

Biological networks

Project	Description	Stars	Conda	PyPI	CRAN	Updated	Paper
Arboreto	A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.	71	531	5,197	-	2024-04-05	Bioinformatics (2019)
Cytoscape	Cytoscape: an open source platform for network analysis and visualization	735	214	-	-	2026-10-09	Genome Res (2003)
pySCENIC	pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference…	646	412	4,466	-	2025-01-09	Nat Protoc (2020)
WGCNA	Weighted Correlation Network Analysis	-	2,214	-	32,832	-	BMC Bioinformatics (2008)

See also: Cell trajectories, markers & regulation; Multi-omics integration.

Omics visualization & exploration

Project	Description	Stars	Conda	Bioconductor	Updated	Paper
ComplexHeatmap	Make Complex Heatmaps	1,561	10,216	48,288	2026-04-02	Bioinformatics (2016)
iSEE	R/shiny interface for interactive visualization of data in SummarizedExperiment objects	231	255	6,161	2026-07-13	F1000Res (2018)

See also: Single-cell analysis & quality.

Footnotes

• Descriptions come from official repositories or package metadata.

• Package mappings and paper references are checked against official sources. One representative paper is linked for each tool, where available.

• Downloads cover the linked packages, including official interfaces. Each cell shows the largest count among the tool’s curated packages in that source; its link identifies the package.

• For software that moved between GitHub repositories, Stars show the highest count among its current and previous official repositories.

• Updated is the committer date of the latest commit on the default or documented development branch.

• A tool may appear in several task groups; Contents counts each tool once.

• Licenses vary, and some tools restrict commercial use; check each project’s terms before use.

Repository metadata: official repositories and package records, including the GitHub REST API. Conda downloads: Anaconda package data, Copyright Anaconda, Inc., CC BY 4.0. PyPI downloads: PyPI Stats, excluding known mirrors. Bioconductor downloads: official package statistics. CRAN downloads: cranlogs, covering the RStudio CRAN mirror.