macOS
Homebrewverified · 100%
brew install samtoolslocal Homebrew formula metadata
MacPortsverified · 94%
sudo port install samtoolsMacPorts ports tree · science/samtools/Portfile · source: api.github.com
brew
Install samtools with Homebrew, apt, dnf, MacPorts, Nix, zypper
Tools for manipulating next-generation sequencing data. Version 1.23.1 via Homebrew; verified 2026-06-22.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install samtoolsDebian stable package indexes · samtools · source: deb.debian.org
Fedora dnfverified · 92%
sudo dnf install samtoolsFedora Rawhide package metadata · samtools · source: dl.fedoraproject.org
Nixverified · 92%
nix profile install nixpkgs#samtoolsnixpkgs package indexes · pkgs/by-name/sa/samtools/package.nix · source: api.github.com
openSUSE zypperverified · 92%
sudo zypper install samtoolsopenSUSE Tumbleweed package metadata · samtools · source: download.opensuse.org
overview
Package summary
Tools for manipulating next-generation sequencing data
Project links
Commands and aliases
- ace2sam
- blast2sam.pl
- bowtie2sam.pl
- export2sam.pl
- fasta-sanitize.pl
- interpolate_sam.pl
- maq2sam-long
- maq2sam-short
- md5fa
- md5sum-lite
- novo2sam.pl
- plot-ampliconstats
- plot-bamstats
- psl2sam.pl
- sam2vcf.pl
- samtools
- samtools.pl
- seq_cache_populate.pl
- soap2sam.pl
- wgsim
- wgsim_eval.pl
- zoom2sam.pl
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.
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 |
|---|---|---|---|
ace2sam | cli | global executable | |
blast2sam.pl | cli | global executable | |
bowtie2sam.pl | cli | global executable | |
export2sam.pl | cli | global executable | |
fasta-sanitize.pl | cli | global executable | |
interpolate_sam.pl | cli | global executable | |
maq2sam-long | cli | global executable | |
maq2sam-short | cli | global executable | |
md5fa | cli | global executable | |
md5sum-lite | cli | global executable | |
novo2sam.pl | cli | global executable | |
plot-ampliconstats | cli | global executable | |
plot-bamstats | cli | global executable | |
psl2sam.pl | cli | global executable | |
sam2vcf.pl | cli | global executable | |
samtools | cli | global executable | |
samtools.pl | cli | global executable | |
seq_cache_populate.pl | cli | global executable | |
soap2sam.pl | cli | global executable | |
wgsim | cli | global executable | |
wgsim_eval.pl | cli | global executable | |
zoom2sam.pl | 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 updated2026-06-22
local dataok
upstreamnot checked
latest detectednot detected
https://github.com/samtools/samtools
- infoNo cached GitHub release or tag data was available.https://github.com/samtools/samtoolsnone confidence
install metadata
Package metadata
| Package key | brew:samtools |
|---|---|
| Version | 1.23.1 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/samtools |
| Homepage | https://www.htslib.org/ |
| Repository | https://github.com/samtools/samtools |
| Upstream docs | https://www.htslib.org/doc |
| License | MIT |
| Source archive | https://github.com/samtools/samtools/releases/download/1.23.1/samtools-1.23.1.tar.bz2 |
| Last updated | 2026-06-22T14:06:14-07:00 |
| Pulse | updated |
| Dependencies | htslib |
| Uses from macOS | ncurses |
| 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 | samtools |
| 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%
samtools 1.21-1
processing sequence alignments in SAM, BAM and CRAM formats
sudo apt install samtools- Section: science
- Architecture: amd64
- 5 dependencies
- 1 optional deps
- normalized package name match
- Matched by: Samtools
Debian apt95%
samtools-test 1.21-1
test files for the samtools package
sudo apt install samtools-test- Section: science
- Architecture: all
- Source Package: samtools
- 1 optional deps
- normalized package name match
- Matched by: Samtools
Nix95%
samtools
nix profile install nixpkgs#samtools- normalized package name match
- Matched by: Samtools
Ubuntu apt95%
samtools 1.19.2-1build2
processing sequence alignments in SAM, BAM and CRAM formats
sudo apt install samtools- Section: universe/science
- Architecture: amd64
- 5 dependencies
- 1 optional deps
- normalized package name match
- Matched by: Samtools
Ubuntu apt95%
samtools-test 1.19.2-1build2
test files for the samtools package
sudo apt install samtools-test- Section: universe/science
- Architecture: all
- Source Package: samtools
- 1 optional deps
- normalized package name match
- Matched by: Samtools
dnf95%
samtools 1.23.1-1.fc45
Tools for nucleotide sequence alignments in the SAM format
sudo dnf install samtools- License: MIT
- Category: Unspecified
- Architecture: x86_64
- Source Package: samtools
- 8 dependencies
- 1 provides
- normalized package name match
- Matched by: Samtools
zypper95%
samtools 1.21-1.3
Tools for manipulating next-generation sequencing data
https://github.com/samtools/samtools
sudo zypper install samtools- License: MIT
- Category: Productivity/Scientific/Other
- Architecture: x86_64
- Source Package: samtools
- 10 dependencies
- 1 provides
- normalized package name match
- Matched by: Samtools
MacPorts95%
samtools
sudo port install samtools- normalized package name match
- Matched by: Samtools
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
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment