# 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 ```sh sudo av install brew:samtools ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install samtools ``` Evidence: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install samtools ``` Evidence: MacPorts ports tree: science/samtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install samtools ``` Evidence: Debian stable package indexes: samtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install samtools ``` Evidence: Fedora Rawhide package metadata: samtools from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/210a2053c8e007daf9ae39c2a21daaed9b2ddd07d63ecffa597050361e73650c-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#samtools ``` Evidence: nixpkgs package indexes: pkgs/by-name/sa/samtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - zypper (92%): ```sh sudo zypper install samtools ``` Evidence: openSUSE Tumbleweed package metadata: samtools from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst ## Package facts - **Package key:** brew:samtools - **Package manager:** Homebrew - **Package manager page:** - **Version:** 1.24 - **Source summary:** Tools for manipulating next-generation sequencing data - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Last updated:** 2026-07-09T19:51:46Z - **Generated:** 2026-08-04T22:13:35+00:00 ## Executables - ace2sam (cli) - blast2sam.pl (cli) - bowtie2sam.pl (cli) - export2sam.pl (cli) - fasta-sanitize.pl (cli) - interpolate_sam.pl (cli) - maq2sam-long (cli) - maq2sam-short (cli) - md5fa (cli) - md5sum-lite (cli) - novo2sam.pl (cli) - plot-ampliconstats (cli) - plot-bamstats (cli) - psl2sam.pl (cli) - sam2vcf.pl (cli) - samtools (cli) - samtools.pl (cli) - seq_cache_populate.pl (cli) - seq_cache_populate.py (cli) - soap2sam.pl (cli) - wgsim (cli) - wgsim_eval.pl (cli) - zoom2sam.pl (cli) - ace2sam (alias) - blast2sam.pl (alias) - bowtie2sam.pl (alias) - export2sam.pl (alias) - fasta-sanitize.pl (alias) - interpolate_sam.pl (alias) - maq2sam-long (alias) - maq2sam-short (alias) - md5fa (alias) - md5sum-lite (alias) - novo2sam.pl (alias) - plot-ampliconstats (alias) - plot-bamstats (alias) - psl2sam.pl (alias) - sam2vcf.pl (alias) - samtools (alias) - samtools.pl (alias) - seq_cache_populate.pl (alias) - seq_cache_populate.py (alias) - soap2sam.pl (alias) - wgsim (alias) - wgsim_eval.pl (alias) - zoom2sam.pl (alias) ## Dependencies - htslib ## Uses from macOS - ncurses ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-08-04 - Package-manager version: 1.24 - Package-manager updated: 2026-07-09 - Local data: ok - Upstream repository: https://github.com/samtools/samtools - info: No cached GitHub release or tag data was available. ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** samtools - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - samtools - 1.21-1: normalized package name match | Debian stable package indexes: samtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | processing sequence alignments in SAM, BAM and CRAM formats | https://www.htslib.org/ - Debian apt - samtools-test - 1.21-1: normalized package name match | Debian stable package indexes: samtools-test from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | test files for the samtools package | https://www.htslib.org/ - Nix - samtools: normalized package name match | nixpkgs package indexes: pkgs/by-name/sa/samtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - samtools - 1.19.2-1build2: normalized package name match | Ubuntu 24.04 LTS package indexes: samtools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | processing sequence alignments in SAM, BAM and CRAM formats | https://www.htslib.org/ - Ubuntu apt - samtools-test - 1.19.2-1build2: normalized package name match | Ubuntu 24.04 LTS package indexes: samtools-test from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | test files for the samtools package | https://www.htslib.org/ - dnf - samtools - 1.24-2.fc45: normalized package name match | Fedora Rawhide package metadata: samtools from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/210a2053c8e007daf9ae39c2a21daaed9b2ddd07d63ecffa597050361e73650c-primary.xml.zst | Tools for nucleotide sequence alignments in the SAM format | http://www.htslib.org/ - zypper - samtools - 1.21-1.5: normalized package name match | openSUSE Tumbleweed package metadata: samtools from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst | Tools for manipulating next-generation sequencing data | https://github.com/samtools/samtools - MacPorts - samtools: normalized package name match | MacPorts ports tree: science/samtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## Related links - [Terminal utility packages](https://pkg.so/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://pkg.so/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Database and data packages](https://pkg.so/database-data-tools/) - Matched database, SQL, migration, or data-store metadata. - [Scientific computing packages](https://pkg.so/scientific-computing-tools/) - Matched scientific computing metadata. - [htslib](https://pkg.so/brew/htslib/) - Runtime dependency declared by Homebrew. - [flye](https://pkg.so/brew/flye/) - Popular package that depends on this formula. - [bcftools](https://pkg.so/brew/bcftools/) - Shares the same upstream homepage. - [sambamba](https://pkg.so/brew/sambamba/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, sam. - [perbase](https://pkg.so/brew/perbase/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics. - [mosdepth](https://pkg.so/brew/mosdepth/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics. - [bedtools](https://pkg.so/brew/bedtools/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science. - [bbtools](https://pkg.so/brew/bbtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [bamtools](https://pkg.so/brew/bamtools/) - Shares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science. - [fgbio](https://pkg.so/brew/fgbio/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science, sequencing. - [blast](https://pkg.so/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. ## Combined YAML source View the package source record on GitHub. [combined/samtools.yml](https://github.com/mxcl/pkgdb/blob/main/combined/samtools.yml) ## Sources - pkg.so package database - Geiger risk classifier - package-page enrichment - package version freshness - pkgdb category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph