Repositories list

• bcftools

  Public
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

  C

  •

  Other

  •258•818•325•11•Updated Oct 29, 2025Oct 29, 2025

• htslib

  Public
  C library for high-throughput sequencing data formats

  bioinformaticsngssam+ 5vcfbamhtslibbcfcram

  C

  •

  Other

  •459•886•139•24•Updated Oct 23, 2025Oct 23, 2025

• samtools

  Public
  Tools (written in C using htslib) for manipulating next-generation sequencing data

  C

  •

  Other

  •603•1.8k•173•17•Updated Oct 23, 2025Oct 23, 2025

• htscodecs

  Public
  Custom compression for CRAM and others.

  C

  •

  Other

  •21•36•0•0•Updated Oct 20, 2025Oct 20, 2025

• htsjdk

  Public
  A Java API for high-throughput sequencing data (HTS) formats.

  javagenomicsngs+ 8sequencingsamvcfdnajava-apifastabam+ 1

  Java

  •243•288•270•42•Updated Sep 26, 2025Sep 26, 2025

• www.htslib.org

  Public
  The http://www.htslib.org/ web site

  HTML

  •13•8•3•0•Updated Sep 25, 2025Sep 25, 2025

• hts-specs

  Public
  Specifications of SAM/BAM and related high-throughput sequencing file formats

  TeX

  •179•689•182•34•Updated Sep 9, 2025Sep 9, 2025

• c-maint

  Public
  Maintenance scripts used with the htslib/samtools/bcftools repositories

  Perl

  •

  Other

  •3•3•0•1•Updated Jul 10, 2025Jul 10, 2025

• htslib-crypt4gh

  Public
  HTSlib crypt4gh plug-in

  C

  •

  Other

  •2•3•1•0•Updated Sep 22, 2023Sep 22, 2023

• klib

  Public
  A standalone and lightweight C library

  C

  •

  MIT License

  •580•0•0•0•Updated Jan 17, 2023Jan 17, 2023

• samtools.github.com

  Public
  The http://samtools.github.io/ (master) and legacy http://samtools.sourceforge.net/ (sf-pages) web sites

  CSS

  •1•4•0•0•Updated Dec 23, 2021Dec 23, 2021

• tabix

  Public archive
  Note: tabix and bgzip binaries are now part of the HTSlib project.

  C

  •38•91•5•2•Updated Aug 3, 2021Aug 3, 2021

• htslib-plugins

  Public
  Plugins for use with HTSlib

  C

  •

  Other

  •8•9•3•0•Updated Mar 19, 2021Mar 19, 2021

• htsjdk-next-beta

  Public
  Staging ground for the development of the next major version of HTSJDK

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •3•6•21•10•Updated Mar 4, 2019Mar 4, 2019

• sapi

  Public
  Sequence Alignment Programming Interface

  C

  •0•7•0•0•Updated Mar 9, 2012Mar 9, 2012