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127 repos shown

List: awesome-bioinformatics

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freebayes/freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Stack

C++ Meson

Updated: 2026-09-03
Lists: 1 list mention
First commit: 2010-02-04
History: 2 history points
License: MIT
Issues: 47 open

880

stars

Forks: 275
Commits: 1,339 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

brentp/mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

AI dev

Stack

Nim

GitHub topics

#coverage #depth #exome #genome #hacktoberfest #nim

Updated: 2026-05-02
Lists: 1 list mention
First commit: 2017-08-17
History: 1 history point
License: MIT
Issues: 50 open

879

stars

Forks: 108
Commits: 257 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

crazyhottommy/ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

Stack

Python

GitHub topics

#chip-seq #histone-modifications #transcription-factor-binding

Updated: 2024-08-05
Lists: 1 list mention
First commit: 2015-06-12
History: 1 history point
License: MIT
Issues: 0 open

855

stars

Forks: 305
Commits: 364 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

chhylp123/hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Stack

C++

GitHub topics

#bioinformatics #denovo-assembly #genomics #hifi-read #pacbio

Updated: 2026-05-31
Lists: 1 list mention
First commit: 2019-05-09
History: 1 history point
License: MIT
Issues: 622 open

818

stars

Forks: 133
Commits: 645 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

BenLangmead/bowtie2

A fast and sensitive gapped read aligner

Stack

C++ CMake

GitHub topics

#bioinformatics #c-plus-plus #genomics #read-aligners

Updated: 2026-09-22
Lists: 1 list mention
First commit: 2011-03-12
History: 1 history point
License: GPL-3.0
Issues: 197 open

811

stars

Forks: 180
Commits: 2,682 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

igvteam/igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

AI dev

Stack

Java Gradle

Updated: 2026-10-21
Lists: 1 list mention
First commit: 2010-11-29
History: 1 history point
License: MIT
Issues: 149 open

768

stars

Forks: 412
Commits: 7,532 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

bebop/poly

A Go package for engineering organisms.

Stack

Go Go modules

GitHub topics

#alignment #bioengineering #bioinformatics #codon-optimizer #computational-biology #dna

Updated: 2026-08-01
Lists: 2 list mentions
First commit: 2020-05-01
History: 2 history points
License: MIT
Issues: 33 open

735

stars

Forks: 72
Commits: 494 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

marbl/canu

A single molecule sequence assembler for genomes large and small.

Stack

C++

Updated: 2026-09-10
Lists: 1 list mention
First commit: 2003-01-02
History: 1 history point
License: Unknown
Issues: 5 open

707

stars

Forks: 181
Commits: 10,523 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Stack

C++ CMake

GitHub topics

#genomics #genotyping #haplotypecaller #variant-calling #vcf-manipulation

Updated: 2026-10-02
Lists: 1 list mention
First commit: 2010-09-22
History: 1 history point
License: MIT
Issues: 17 open

687

stars

Forks: 223
Commits: 1,699 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

oschwengers/bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Stack

Python pip

GitHub topics

#annotation #bacteria #bacterial-genomes #bioinformatics #genome-annotation #mag

Updated: 2026-10-11
Lists: 1 list mention
First commit: 2020-01-15
History: 1 history point
License: GPL-3.0
Issues: 29 open

686

stars

Forks: 88
Commits: 1,104 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

mattgodbolt/zindex

Create an index on a compressed text file

Stack

C++ CMake

Updated: 2026-10-20
Lists: 1 list mention
First commit: 2015-02-23
History: 1 history point
License: BSD-2-Clause
Issues: 19 open

658

stars

Forks: 39
Commits: 213 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Stack

Java Maven

GitHub topics

#bioinformatics #genomics #java #parser-library #pdb #protein-data-bank

Updated: 2026-09-29
Lists: 1 list mention
First commit: 2009-09-15
History: 1 history point
License: LGPL-2.1
Issues: 70 open

634

stars

Forks: 400
Commits: 7,058 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

s-andrews/FastQC

A quality control analysis tool for high throughput sequencing data

Stack

Java

Updated: 2026-10-07
Lists: 1 list mention
First commit: 2017-12-21
History: 1 history point
License: GPL-3.0
Issues: 24 open

624

stars

Forks: 124
Commits: 211 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

insitro/redun

Yet another redundant workflow engine

Stack

Python Jupyter pytest pip uv

GitHub topics

#aws #bioinformatics #data-engineering #data-science #docker #etl

Updated: 2026-07-17
Lists: 1 list mention
First commit: 2021-10-08
History: 1 history point
License: Apache-2.0
Issues: 34 open

605

stars

Forks: 53
Commits: 511 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

NBISweden/AGAT

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

Stack

HTML pip

GitHub topics

#agat #gff #gff-format #gtf #perl-scripts #standardisation

Updated: 2026-09-07
Lists: 1 list mention
First commit: 2019-11-15
History: 1 history point
License: GPL-3.0
Issues: 27 open

588

stars

Forks: 65
Commits: 588 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

mummer4/mummer

Mummer alignment tool

Stack

C++

Updated: 2025-02-04
Lists: 1 list mention
First commit: 2012-11-08
History: 1 history point
License: Artistic-2.0
Issues: 167 open

578

stars

Forks: 119
Commits: 340 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

vcftools/vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Stack

C++

Updated: 2025-05-15
Lists: 1 list mention
First commit: 2015-06-25
History: 1 history point
License: LGPL-3.0
Issues: 122 open

565

stars

Forks: 153
Commits: 137 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

teamdfir/sift

SIFT

GitHub topics

#aws #cast #cast-distro #cli #forensics #issues-only

Updated: 2024-02-14
Lists: 1 list mention
First commit: 2015-02-09
History: 1 history point
License: MIT
Issues: 20 open

554

stars

Forks: 67
Commits: 31 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

dellytools/delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Stack

C++ PEP 517

GitHub topics

#cancer-genomics #delly #delly-users #genomic #germline #rearrangement

Updated: 2026-10-14
Lists: 1 list mention
First commit: 2013-11-15
History: 1 history point
License: BSD-3-Clause
Issues: 41 open

538

stars

Forks: 139
Commits: 1,577 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

ruanjue/wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Stack

GitHub topics

#alignment #assembly #nanopore #pacbio

Updated: 2023-09-27
Lists: 1 list mention
First commit: 2017-09-29
History: 1 history point
License: GPL-3.0
Issues: 42 open

533

stars

Forks: 93
Commits: 437 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

bactopia/bactopia

A flexible pipeline for complete analysis of bacterial genomes

AI dev

Stack

Nextflow

GitHub topics

#bacterial-genomes #bioconda #conda #fastqs #nextflow

Updated: 2026-08-05
Lists: 1 list mention
First commit: 2019-02-22
History: 1 history point
License: MIT
Issues: 70 open

523

stars

Forks: 82
Commits: 1,634 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

jtleek/genomicspapers

The Leek group guide to genomics papers

Updated: 2018-11-05
Lists: 1 list mention
First commit: 2014-10-07
History: 1 history point
License: Unknown
Issues: 3 open

504

stars

Forks: 175
Commits: 18 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

biojs/biojs

🔬A library of JavaScript components to represent biological data

GitHub topics

#biojs #biology #javascript #visualisation

Updated: 2021-10-11
Lists: 1 list mention
First commit: 2014-08-01
History: 1 history point
License: Apache-2.0
Issues: 57 open

503

stars

Forks: 117
Commits: 321 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

Stack

Python PEP 517 pip

GitHub topics

#bgzf #bioinformatics #dna #fasta #genomics #indexing

Updated: 2026-10-21
Lists: 1 list mention
First commit: 2013-09-12
History: 1 history point
License: NOASSERTION
Issues: 3 open

489

stars

Forks: 80
Commits: 938 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

deweylab/RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

Stack

C++

Updated: 2026-08-07
Lists: 1 list mention
First commit: 2011-02-09
History: 1 history point
License: GPL-3.0
Issues: 145 open

479

stars

Forks: 122
Commits: 518 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

GMOD/jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

Stack

JavaScript Electron Express React npm pip Yarn

GitHub topics

#bioinformatics #biology #genome-annotation #genome-browser #genomics #protein-annotation

Updated: 2026-07-16
Lists: 1 list mention
First commit: 2007-06-18
History: 1 history point
License: NOASSERTION
Issues: 158 open

474

stars

Forks: 199
Commits: 8,175 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

Illumina/manta

Structural variant and indel caller for mapped sequencing data

Archived

Stack

C++ CMake

GitHub topics

#bioinformatics #indels #structural-variation #structural-variations

Updated: 2025-10-11
Lists: 1 list mention
First commit: 2013-05-30
History: 1 history point
License: NOASSERTION
Issues: 130 open

467

stars

Forks: 160
Commits: 2,634 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

seqan/seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Stack

C++ CMake

GitHub topics

#bioinformatics #blast #cpp-concepts #cpp20 #fasta #fastq

Updated: 2026-10-17
Lists: 1 list mention
First commit: 2017-03-17
History: 1 history point
License: NOASSERTION
Issues: 33 open

465

stars

Forks: 89
Commits: 7,116 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

Website GitHub

brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

Stack

Cython CMake PEP 517 pip

GitHub topics

#bioinformatics #cython #genomics #htslib #vcf

Updated: 2026-09-10
Lists: 1 list mention
First commit: 2015-08-12
History: 1 history point
License: MIT
Issues: 51 open

450

stars

Forks: 79
Commits: 552 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

pezmaster31/bamtools

C++ API & command-line toolkit for working with BAM data

Stack

C++ CMake

Updated: 2025-05-18
Lists: 1 list mention
First commit: 2009-04-10
History: 1 history point
License: MIT
Issues: 72 open

432

stars

Forks: 154
Commits: 519 commits
Star growth, last 7 days: 0 0.0%
Commit velocity, last 7 days: 0 0.0%

GitHub

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