# Install salmon with Homebrew, apt, Nix Transcript-level quantification from RNA-seq reads. Version 2.4.1 via Homebrew; verified 2026-07-30. Also installable with debian: sudo apt install salmon. ## Install ```sh sudo av install brew:salmon ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install salmon ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install salmon ``` Evidence: Debian stable package indexes: salmon from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#salmon ``` Evidence: nixpkgs package indexes: pkgs/by-name/sa/salmon/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:salmon - **Package manager:** Homebrew - **Version:** 2.4.1 - **Source summary:** Transcript-level quantification from RNA-seq reads - **Homepage:** - **Repository:** - **Last updated:** 2026-07-30T01:26:57Z - **Generated:** 2026-08-03T19:37:03+00:00 ## Executables - salmon (alias) ## Install behavior - Bottle: not available ## Freshness - Page generated: 2026-08-03 - Package-manager version: 2.4.1 ## Project history and usage salmon is a COMBINE-lab command-line tool for fast, accurate transcript-level quantification from RNA-seq reads. Its current official documentation describes the core workflow as building a reusable transcriptome index with `salmon index`, quantifying reads with `salmon quant`, and consuming the resulting `quant.sf` abundance table in downstream RNA-seq tooling. ### Project history The project is tied to the 2017 Nature Methods paper by Patro, Duggal, Love, Irizarry, and Kingsford, which the official docs and README ask users to cite. The original C++ salmon line became a common bulk RNA-seq quantifier, with selective alignment becoming the default mapping strategy from the 1.0.0 line according to the legacy official documentation. In 2026 the project released salmon 2.0, a from-scratch Rust rewrite. Official release notes say the rewrite kept the familiar `salmon index` to `salmon quant` to `quant.sf` workflow and downstream output formats while moving to a single portable binary and adding an alignment-free `--sketch` mode. ### Adoption history salmon is packaged across multiple package-manager ecosystems in the supplied package facts, including Homebrew, Debian, Ubuntu, and Nix. The official installation docs also document install-script binaries, Cargo, conda/Bioconda, Docker Hub, and GHCR images, reflecting its use in reproducible computational-biology pipelines. The official docs describe `quant.sf` as directly readable by tximport, tximeta, fishpond, and swish, which is why salmon appears frequently in RNA-seq analysis workflows as a quantification stage rather than as a standalone end-user application. ### How it is used Typical use is to build an index from transcript FASTA input, quantify single-end or paired-end FASTQ reads against that index, and read transcript-level abundance estimates from `quant.sf`. The CLI also supports transcriptome BAM input, RAD input, bias correction flags, bootstraps or Gibbs samples for uncertainty, gene-level output via a transcript-to-gene map, and `quantmerge` for combining columns across samples. ### Why package nerds care salmon matters to package maintainers because it sits at the intersection of scientific CLI distribution and performance-sensitive native code. The 2.x Rust rewrite reduced the historic C++ dependency burden while preserving command names and output files, which makes package upgrades easier but still requires users to rebuild old C++ indices. ### Timeline - 2017: Salmon Nature Methods paper published and cited by the official project docs. - 1.0.0 line: Selective alignment becomes the default mapping strategy according to the official legacy docs. - 2026-06-13: salmon 2.0.0 released as the first Rust rewrite, retaining the index/quant/quant.sf workflow. - 2026-06-23: legacy C++ v1.12.1 release notes recommend 2.x for bulk RNA-seq and reserve 1.x for users needing the original C++ implementation. - 2026-07-02: GitHub lists v2.3.1 as the latest release. ### Related projects - Official docs name tximport, tximeta, fishpond, and swish as downstream tools that consume salmon output. They also point users of the removed historical `salmon alevin` single-cell workflow to the alevin-fry ecosystem. ### Sources - Official CLI reference: https://combine-lab.github.io/salmon/reference/cli/ - Official GitHub README/releases: https://github.com/COMBINE-lab/salmon - Official docs introduction: https://combine-lab.github.io/salmon/getting-started/introduction/ - Official docs: https://combine-lab.github.io/salmon/ - Supplied input fields: source_facts.package-manager, source_facts.description, source_facts.repo ## Security Notes No matching local secret-handling manifest was found for salmon. Nucleus package metadata is still published here so future coverage has a stable package URL. ## Other Package-Manager Records - Debian apt - salmon - 1.10.2+ds1-1+b5: normalized package name match | Debian stable package indexes: salmon from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | wicked-fast transcript quantification from RNA-seq data | https://github.com/COMBINE-lab/salmon - Nix - salmon: normalized package name match | nixpkgs package indexes: pkgs/by-name/sa/salmon/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - salmon - 1.10.2+ds1-1build2: normalized package name match | Ubuntu 24.04 LTS package indexes: salmon from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | wicked-fast transcript quantification from RNA-seq data | https://github.com/COMBINE-lab/salmon ## Combined YAML source View the package source record on GitHub. [combined/salmon.yml](https://github.com/mxcl/pkgdb/blob/main/combined/salmon.yml) ## Sources - pkg.so package database - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph