macOS
Homebrewverified · 100%
brew install htsliblocal Homebrew formula metadata
MacPortsverified · 94%
sudo port install htslibMacPorts ports tree · science/htslib/Portfile · source: api.github.com
brew
Install htslib with Homebrew, apt, dnf, MacPorts, Nix, zypper
C library for high-throughput sequencing data formats. Version 1.23.1 via Homebrew; verified from local package data.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install htslib-testDebian stable package indexes · htslib-test · source: deb.debian.org
Fedora dnfverified · 92%
sudo dnf install htslibFedora Rawhide package metadata · htslib · source: dl.fedoraproject.org
Nixverified · 92%
nix profile install nixpkgs#htslibnixpkgs package indexes · pkgs/by-name/ht/htslib/package.nix · source: api.github.com
openSUSE zypperverified · 92%
sudo zypper install bgzipopenSUSE Tumbleweed package metadata · bgzip · source: download.opensuse.org
overview
Package summary
C library for high-throughput sequencing data formats
Project links
Commands and aliases
- annot-tsv
- bgzip
- htsfile
- ref-cache
- tabix
history
Project history and usage
HTSlib is the C library layer of the Samtools family, providing shared reading and writing support for high-throughput sequencing formats such as SAM, BAM, CRAM, VCF, and BCF. It matters beyond a single command-line package because many genomics tools build on the same file-format and indexing behavior.
Project history
The Samtools site describes the project as three related repositories: Samtools for alignment manipulation, BCFtools for variant data, and HTSlib as the common C library. Its download page preserves the split in historical context, noting that before HTSlib was introduced, Samtools and BCFtools were shipped together in a single samtools-0.1.x source package.
The annotated 1.0 tag in the official GitHub repository, dated 2014-08-15, describes the first HTSlib release as supporting SAM, BAM, CRAM, VCF, and BCF. Later release notes show the library continuing to absorb format, indexing, threading, remote-I/O, and ABI changes that affect downstream tools.
Adoption history
HTSlib's adoption is tightly coupled to the Samtools ecosystem: the Samtools site says Samtools and BCFtools use HTSlib internally, while HTSlib is also distributed separately for developers writing programs against its API. Packaging across Homebrew, Debian-family distributions, Fedora, MacPorts, Nix, and openSUSE reflects its role as a build-time and runtime dependency rather than only an end-user utility.
How it is used
Package users often encounter HTSlib through utilities installed with the library, especially bgzip, htsfile, tabix, ref-cache, and annot-tsv. Developers use the C API for compressed genomic files, indexes, region queries, remote access, and format detection in sequencing and variant-analysis workflows.
Why package nerds care
HTSlib is package-nerd significant because it is both a library ABI and a bundle of small Unix-style genomics tools. Changes such as the 2019 1.10 release's SAM header API, multi-threaded SAM I/O, on-the-fly indexing, S3 updates, and 64-bit reference-position support are the sort of low-level package events that can ripple through many bioinformatics builds.
Timeline
- 2012: The samtools/htslib repository was created on GitHub.
- 2014: The 1.0 tag marked the first HTSlib release, supporting SAM, BAM, CRAM, VCF, and BCF.
- 2019: Release 1.10 added a SAM header API, multi-threaded SAM reading and writing, on-the-fly indexing, and S3 interface updates.
- 2026: Release notes for 1.23.1 documented CRAM decoder security fixes and related build updates.
Related projects
- Samtools and BCFtools are the closest sibling projects, both using HTSlib internally. Related file-format work includes the SAM, BAM, CRAM, VCF, BCF, BGZF, and tabix indexing formats that HTSlib reads, writes, or helps index.
Sources
- Samtools project site, HTSlib download notes, GitHub repository metadata, and official release/tag metadata.
security posture
Risk level: green
library-like package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- library-like package without higher-risk signals
Signals
- metadata:library-like
Install behavior
- No Homebrew post-install hook is recorded in formula metadata.
- Homebrew bottle metadata is available for 6 platform targets.
- Installs with 2 runtime dependencies.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
annot-tsv | cli | global executable | |
bgzip | cli | global executable | |
htsfile | cli | global executable | |
ref-cache | cli | global executable | |
tabix | cli | global executable |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-07-08
manager version1.23.1
manager updated
local dataok
upstreamnot checked
latest detectednot detected
https://github.com/samtools/htslib
- infoNo package-manager update timestamp was available.low confidence
- infoNo cached GitHub release or tag data was available.https://github.com/samtools/htslibnone confidence
install metadata
Package metadata
| Package key | brew:htslib |
|---|---|
| Version | 1.23.1 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/htslib |
| Homepage | https://www.htslib.org/ |
| Repository | https://github.com/samtools/htslib |
| Upstream docs | https://github.com/samtools/htslib#readme |
| License | MIT AND BSD-3-Clause |
| Source archive | https://github.com/samtools/htslib/releases/download/1.23.1/htslib-1.23.1.tar.bz2 |
| Dependencies | libdeflate, xz |
| Uses from macOS | bzip2, curl |
| Bottle | available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | htslib |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
htslib-test 1.21+ds-1
Test data for HTSlib
https://github.com/samtools/htslib
sudo apt install htslib-test- Section: libs
- Architecture: all
- Source Package: htslib
- 1 dependencies
- normalized package name match
- Matched by: Htslib
Debian apt95%
libhts-dev 1.21+ds-1
development files for the HTSlib
https://github.com/samtools/htslib
sudo apt install libhts-dev- Section: libdevel
- Architecture: amd64
- Source Package: htslib
- 6 dependencies
- normalized package name match
- Matched by: Htslib
Debian apt95%
libhts3t64 1.21+ds-1
C library for high-throughput sequencing data formats
https://github.com/samtools/htslib
sudo apt install libhts3t64- Section: libs
- Architecture: amd64
- Source Package: htslib
- 8 dependencies
- 1 provides
- normalized package name match
- Matched by: Htslib
Debian apt95%
tabix 1.21+ds-1
generic indexer for TAB-delimited genome position files
https://github.com/samtools/htslib
sudo apt install tabix- Section: science
- Architecture: amd64
- Source Package: htslib
- 6 dependencies
- normalized package name match
- Matched by: Htslib
Nix95%
htslib
nix profile install nixpkgs#htslib- normalized package name match
- Matched by: Htslib
Ubuntu apt95%
htslib-test 1.19+ds-1.1build3
Test data for HTSlib
https://github.com/samtools/htslib
sudo apt install htslib-test- Section: universe/libs
- Architecture: all
- Source Package: htslib
- 1 dependencies
- normalized package name match
- Matched by: Htslib
Ubuntu apt95%
libhts-dev 1.19+ds-1.1build3
development files for the HTSlib
https://github.com/samtools/htslib
sudo apt install libhts-dev- Section: universe/libdevel
- Architecture: amd64
- Source Package: htslib
- 5 dependencies
- normalized package name match
- Matched by: Htslib
Ubuntu apt95%
libhts3t64 1.19+ds-1.1build3
C library for high-throughput sequencing data formats
https://github.com/samtools/htslib
sudo apt install libhts3t64- Section: universe/libs
- Architecture: amd64
- Source Package: htslib
- 8 dependencies
- 1 provides
- normalized package name match
- Matched by: Htslib
Ubuntu apt95%
tabix 1.19+ds-1.1build3
generic indexer for TAB-delimited genome position files
https://github.com/samtools/htslib
sudo apt install tabix- Section: universe/science
- Architecture: amd64
- Source Package: htslib
- 6 dependencies
- normalized package name match
- Matched by: Htslib
dnf95%
htslib 1.23.1-2.fc45
C library for high-throughput sequencing data formats
sudo dnf install htslib- License: MIT AND BSD-3-Clause AND LicenseRef-Fedora-Public-Domain
- Category: Unspecified
- Architecture: i686
- Source Package: htslib
- 8 dependencies
- 2 provides
- normalized package name match
- Matched by: Htslib
dnf95%
htslib-devel 1.23.1-2.fc45
Development files for htslib
sudo dnf install htslib-devel- License: MIT AND BSD-3-Clause AND LicenseRef-Fedora-Public-Domain
- Category: Unspecified
- Architecture: i686
- Source Package: htslib
- 3 dependencies
- 2 provides
- normalized package name match
- Matched by: Htslib
dnf95%
htslib-tools 1.23.1-2.fc45
Additional htslib-based tools
sudo dnf install htslib-tools- License: MIT AND BSD-3-Clause AND LicenseRef-Fedora-Public-Domain
- Category: Unspecified
- Architecture: x86_64
- Source Package: htslib
- 8 dependencies
- 1 provides
- normalized package name match
- Matched by: Htslib
MacPorts95%
htslib
sudo port install htslib- normalized package name match
- Matched by: Htslib
zypper92%
bgzip 1.21-1.3
Block compression/decompression utility from the HTSlib project
https://github.com/samtools/htslib/
sudo zypper install bgzip- License: MIT
- Category: Productivity/Scientific/Other
- Architecture: x86_64
- Source Package: libhts
- 8 dependencies
- 1 provides
- installed executable or alias match
- Matched by: Bgzip
zypper92%
htsfile 1.21-1.3
Identify high-throughput sequencing data files from the HTSlib project
https://github.com/samtools/htslib/
sudo zypper install htsfile- License: MIT
- Category: Productivity/Scientific/Other
- Architecture: x86_64
- Source Package: libhts
- 9 dependencies
- 1 provides
- installed executable or alias match
- Matched by: Htsfile
zypper92%
tabix 1.21-1.3
Generic indexer for TAB-delimited genome position files from the HTSlib project
https://github.com/samtools/htslib/
sudo zypper install tabix- License: MIT
- Category: Productivity/Scientific/Other
- Architecture: x86_64
- Source Package: libhts
- 10 dependencies
- 1 provides
- installed executable or alias match
- Matched by: Tabix
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment