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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

cram-js

Read CRAM v3 and v2 in node or in the browser

cram31_bench

Scripts for the CRAM 3.1 paper benchmarking

cram_conformance

Test files for validating a CRAM decoder

crumble

Exploration of controlled loss of quality values for compressing CRAM files

fqzcomp

Fastq compression tool

fqzcomp5

gdcc

hts-specs

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

htscodecs

Custom compression for CRAM and others.

htscodecs-corpus

A larger set of test data for htscodecs

htslib

C library for high-throughput sequencing data formats

htslib_benchmark

Benchmarking of htslib and other tools

io_lib

Staden Package "io_lib" (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.

io_trace

Summarises strace output

ioccc_2002b

A *failed* IOCCC entry for 2002

klib

A standalone and lightweight C library

mpeg_misc

Miscellaneous scripts and code for working on the MPEG genome-compression AHG

qual_smooth

quantum-explorers

A self-paced, quantum computing learning journey for high school students and above.

rans_static

rANS coder (derived from https://github.com/rygorous/ryg_rans)

sam_realigner

Realigns SAM/BAM/CRAM files to fix pairwise vs multiple alignment issues.

samtools

Samtools with CRAM support (inherited from staden package io_lib).

tabix

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

turbobench

TurboBench Compression Benchmark

www.htslib.org

The htslib.org web site

zlib

A massively spiffy yet delicately unobtrusive compression library.