Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

Conda recipes for the bioconda channel.

C library for high-throughput sequencing data formats

GA4GH Refget specifications docs

Draft changes to SAM/BAM and related high-throughput sequencing specifications

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

TASC aids the harmonisation of aspects of GA4GH's various products that would otherwise prevent different products from being used together conveniently.

Custom compression for CRAM and others.

The Python programming language

Official code repository for GATK versions 4 and up

Documentation for bioconda

Burrow-Wheeler Aligner

Utilities for building and managing bioconda recipes

Static checker for GitHub Actions workflow files

A powerful toolset for genome arithmetic.

A standalone and lightweight C library

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

A fast and clever hex editor for macOS

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.

Annotation of Genetic Variants

The htslib.org web site

The open-source repo for docs.github.com