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samtools

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

htslib

C library for high-throughput sequencing data formats

hts-specs

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

bcftools

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

htsjdk

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

tabix

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

htscodecs

Custom compression for CRAM and others.

htslib-plugins

Plugins for use with HTSlib

www.htslib.org

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

htsjdk-next-beta

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

sapi

Sequence Alignment Programming Interface

samtools.github.com

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

c-maint

Maintenance scripts used with the htslib/samtools/bcftools repositories

htslib-crypt4gh

HTSlib crypt4gh plug-in