Automic VaultAutomic Vault

brew

Install bamtools with Homebrew, apt, MacPorts, Nix

C++ API and command-line toolkit for BAM data. Version 2.5.3 via Homebrew; verified 2026-05-03.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install bamtools

local Homebrew formula metadata

MacPortsverified · 94%
sudo port install bamtools

MacPorts ports tree · devel/bamtools/Portfile · source: api.github.com

Linux

Debian aptverified · 92%
sudo apt install bamtools

Debian stable package indexes · bamtools · source: deb.debian.org

Nixverified · 92%
nix profile install nixpkgs#bamtools

nixpkgs package indexes · pkgs/by-name/ba/bamtools/package.nix · source: api.github.com

overview

Package summary

C++ API and command-line toolkit for BAM data

Commands and aliases

  • bamtools

history

Project history and usage

BamTools is a C++ API and command-line toolkit for working with BAM files, the binary alignment format used throughout high-throughput sequencing workflows. It is a packaging-significant bioinformatics utility because it provides both reusable libraries and small CLI tools for common BAM inspection and transformation jobs.

Project history

The official repository history begins in April 2009 with an initial import by the BamTools maintainers. The README identifies BamTools as both a programmer's API and an end-user toolkit for BAM files and credits Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg in the 2009-2010 copyright notice.

The README explicitly acknowledges Heng Li's SAMtools as the original C-language BAM API and toolkit, placing BamTools in the second wave of tooling around the SAM/BAM ecosystem: a C++ library and CLI layer for developers and pipeline authors who wanted BAM manipulation without binding directly to SAMtools internals.

BamTools reached the 2.x series by 2011 and has continued to receive maintenance releases, including the 2.5.x line used by modern package managers.

Adoption history

BamTools became a routine distribution package for bioinformatics environments: the supplied package facts list Homebrew, Debian/Ubuntu, MacPorts, and Nix packages. That adoption matters because genomics pipelines often rely on system packages for reproducible command-line utilities on shared clusters and CI images.

How it is used

The source tree builds a bamtools toolkit binary with subcommands such as convert, count, coverage, filter, header, index, merge, random, resolve, revert, sort, split, and stats. The same repository also exposes a C++ API for applications that need to read or write BAM data programmatically.

Typical users are bioinformatics developers, sequencing pipeline maintainers, and researchers doing command-line BAM file processing outside larger workflow systems.

Why package nerds care

For package nerds, BamTools sits at the intersection of library packaging and scientific reproducibility. It is small enough to be a normal Unix package but domain-specific enough that ABI, zlib linkage, and command compatibility matter to downstream genomics stacks.

Its relationship to SAMtools makes it historically useful: SAMtools became the canonical C toolkit, while BamTools offered a C++-oriented alternative that distributions could ship for software expecting the BamTools API.

Timeline

  • 2009: Initial BamTools import appears in the official Git history.
  • 2009-2010: README copyright credits the original BamTools authors.
  • 2011: v2.0.0 is tagged, establishing the 2.x API/toolkit line.
  • 2017: v2.5.1 is tagged in the long-lived 2.5 series.
  • 2025: v2.5.3 is tagged as a maintenance release.

Related projects

  • BamTools is directly related to SAMtools and the SAM/BAM file-format ecosystem. It is commonly adjacent to HTSlib/SAMtools-style tooling, alignment pipelines, and downstream genomics packages that consume BAM files.

security posture

Risk level: green

narrow executable package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • narrow executable package without higher-risk signals

Signals

  • metadata:no-higher-risk-signals

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Installs with 1 runtime dependencies.
  • Build metadata lists 2 build 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

CommandKindExposureNote
bamtoolscliglobal 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 version2.5.3
manager updated2026-05-03
local dataok
upstreamcurrent
latest detectedv2.5.3

https://github.com/pezmaster31/bamtools

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:bamtools
Version2.5.3
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/bamtools
Homepagehttps://github.com/pezmaster31/bamtools
Repositoryhttps://github.com/pezmaster31/bamtools
Upstream docshttps://github.com/pezmaster31/bamtools/wiki
LicenseMIT
Source archivehttps://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.3.tar.gz
Last updated2026-05-03T16:10:34Z
Pulseupdated
Dependenciesjsoncpp
Build dependenciescmake, pkgconf
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namebamtools
Version Scheme0
Revision1
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

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%

bamtools 2.5.2+dfsg-6+b1

toolkit for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install bamtools
  • Section: science
  • Architecture: amd64
  • Source Package: bamtools
  • 5 dependencies
  • normalized package name match
  • Matched by: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: bamtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

libbamtools-dev 2.5.2+dfsg-6+b1

C++ API for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install libbamtools-dev
  • Section: libdevel
  • Architecture: amd64
  • Source Package: bamtools
  • 2 dependencies
  • 1 optional deps
  • normalized package name match
  • Matched by: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbamtools-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

libbamtools-doc 2.5.2+dfsg-6

docs for dynamic library for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install libbamtools-doc
  • Section: doc
  • Architecture: all
  • Source Package: bamtools
  • 1 dependencies
  • normalized package name match
  • Matched by: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbamtools-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

libbamtools2.5.2 2.5.2+dfsg-6+b1

dynamic library for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install libbamtools2.5.2
  • Section: libs
  • Architecture: amd64
  • Source Package: bamtools
  • 4 dependencies
  • normalized package name match
  • Matched by: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbamtools2.5.2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

bamtools

nix profile install nixpkgs#bamtools
  • normalized package name match
  • Matched by: Bamtools
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/ba/bamtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

bamtools 2.5.2+dfsg-4

toolkit for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install bamtools
  • Section: universe/science
  • Architecture: amd64
  • 5 dependencies
  • normalized package name match
  • Matched by: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: bamtools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

libbamtools-dev 2.5.2+dfsg-4

C++ API for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install libbamtools-dev
  • Section: universe/libdevel
  • Architecture: amd64
  • Source Package: bamtools
  • 2 dependencies
  • 1 optional deps
  • normalized package name match
  • Matched by: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbamtools-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

libbamtools-doc 2.5.2+dfsg-4

docs for dynamic library for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install libbamtools-doc
  • Section: universe/doc
  • Architecture: all
  • Source Package: bamtools
  • 1 dependencies
  • normalized package name match
  • Matched by: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbamtools-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

libbamtools2.5.2 2.5.2+dfsg-4

dynamic library for manipulating BAM (genome alignment) files

https://github.com/pezmaster31/bamtools/wiki

sudo apt install libbamtools2.5.2
  • Section: universe/libs
  • Architecture: amd64
  • Source Package: bamtools
  • 4 dependencies
  • normalized package name match
  • Matched by: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbamtools2.5.2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
MacPorts95%

bamtools

sudo port install bamtools
  • normalized package name match
  • Matched by: Bamtools
MacPorts ports tree · api.github.com · MacPorts ports tree: devel/bamtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • cmakeBuild dependency declared by Homebrew.
  • pkgconfBuild dependency declared by Homebrew.
  • augustusPopular package that depends on this formula.

Same workflow

  • perbaseShares av.db curated category or tags: bam, bioinformatics, cli, science.
  • sambambaShares av.db curated category or tags: bam, bioinformatics, cli, science.
  • samtoolsShares av.db curated category or tags: bam, bioinformatics, cli, science.
  • abpoaShares av.db curated category or tags: bioinformatics, cli, science.
  • abricateShares av.db curated category or tags: bioinformatics, cli, science.
  • abyssShares av.db curated category or tags: bioinformatics, cli, science.

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.

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