samtools

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

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

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

C library for high-throughput sequencing data formats

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

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

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

Maintenance scripts used with the htslib/samtools/bcftools repositories

Plugins for use with HTSlib

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

Sequence Alignment Programming Interface