使用 Homebrew, apt, Nix 安装 salmon

项目链接

• 主页

命令和别名

• salmon

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

• 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.

来源

• 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