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 / rank 1852
Install samtools with Homebrew, apt, dnf, MacPorts, Nix, zypper
Tools for manipulating next-generation sequencing data. Version 1.24 via Homebrew; verified 2026-07-09. Also installable with debian: sudo apt install samtools.
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
- seq_cache_populate.py
- 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 bottle metadata was recorded.
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 | executable | indexed executable | Discovered from the local executable index. |
blast2sam.pl | executable | indexed executable | Discovered from the local executable index. |
bowtie2sam.pl | executable | indexed executable | Discovered from the local executable index. |
export2sam.pl | executable | indexed executable | Discovered from the local executable index. |
fasta-sanitize.pl | executable | indexed executable | Discovered from the local executable index. |
interpolate_sam.pl | executable | indexed executable | Discovered from the local executable index. |
maq2sam-long | executable | indexed executable | Discovered from the local executable index. |
maq2sam-short | executable | indexed executable | Discovered from the local executable index. |
md5fa | executable | indexed executable | Discovered from the local executable index. |
md5sum-lite | executable | indexed executable | Discovered from the local executable index. |
novo2sam.pl | executable | indexed executable | Discovered from the local executable index. |
plot-ampliconstats | executable | indexed executable | Discovered from the local executable index. |
plot-bamstats | executable | indexed executable | Discovered from the local executable index. |
psl2sam.pl | executable | indexed executable | Discovered from the local executable index. |
sam2vcf.pl | executable | indexed executable | Discovered from the local executable index. |
samtools | executable | indexed executable | Discovered from the local executable index. |
samtools.pl | executable | indexed executable | Discovered from the local executable index. |
seq_cache_populate.pl | executable | indexed executable | Discovered from the local executable index. |
seq_cache_populate.py | executable | indexed executable | Discovered from the local executable index. |
soap2sam.pl | executable | indexed executable | Discovered from the local executable index. |
wgsim | executable | indexed executable | Discovered from the local executable index. |
wgsim_eval.pl | executable | indexed executable | Discovered from the local executable index. |
zoom2sam.pl | executable | indexed executable | Discovered from the local executable index. |
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 generated2026-08-03
manager version1.24
manager updated2026-07-09
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:samtools |
|---|---|
| Version | 1.24 |
| Package manager | Homebrew |
| Homepage | https://www.htslib.org/ |
| Repository | https://github.com/samtools/samtools |
| Last updated | 2026-07-09T19:51:46Z |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
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 1.24-2.fc45
Tools for nucleotide sequence alignments in the SAM format
sudo dnf install samtools- License: MIT
- Category: Unspecified
- Architecture: x86_64
- Source Package: samtools
- 10 dependencies
- 1 provides
- normalized package name match
- Matched by: Samtools
zypper95%
samtools 1.21-1.5
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
- cross-ecosystem install command graph
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation