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bambi

A set of programs to manipulate SAM/BAM/CRAM files, using HTSLIB

bamtools

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

bcftools

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

bwa

Burrow-Wheeler Aligner

hts-binaries

Build script to make binary distributions of HTSlib, samtools and bcftools

hts-specs

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

htscodecs

Custom compression for CRAM and others.

htslib

C library for high-throughput sequencing data formats. This is not the official repository, see samtools/htslib for that.

htslib-crypt4gh

HTSlib crypt4gh plug-in

klib

A standalone and lightweight C library

manconvert

Convert troff-style man pages to doxygen source or formatted HTML

mmonitor

Very simple memory monitor

openssh-portable

Portable OpenSSH

oss-fuzz

OSS-Fuzz - continuous fuzzing of open source software.

pthread_mon

Pthreads locking monitor

qu-mfeindex

DNA sequence indexer originally developed for MFEprimer-2.0. This is not the official repository, see quwubin/qu-mfeindex for that.

ref-cache-nginx

Configuration files for the nginx web server to make a CRAM reference sequence cache

samtools

This is not the official development repository for samtools. For that you should use samtools/samtools.

teepot

vcf-validator

Validator for VCF implemented using C++11

vgp-tools

viralconsensus

Fast viral consensus genome reconstruction

www.htslib.org

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