# salmon を Homebrew, apt, Nix でインストール

salmon のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。

## インストール

```sh
sudo av install brew:salmon
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install salmon
```

  証拠: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install salmon
```

  証拠: 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
```

  証拠: nixpkgs package indexes: pkgs/by-name/sa/salmon/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

## パッケージ情報

- **パッケージキー:** brew:salmon
- **パッケージマネージャ:** Homebrew
- **バージョン:** 2.4.1
- **ソース概要:** Transcript-level quantification from RNA-seq reads
- **ホームページ:** <https://github.com/COMBINE-lab/salmon>
- **リポジトリ:** <https://github.com/COMBINE-lab/salmon>
- **最終更新:** 2026-07-30T01:26:57Z
- **生成日時:** 2026-08-03T19:37:03+00:00

## 実行可能ファイル

- salmon (エイリアス)

## インストール挙動

- Bottle: 利用不可

## バージョンと鮮度

- ページ生成日: 2026-08-03
- マネージャ版: 2.4.1
## プロジェクトの歴史と使われ方

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.

### プロジェクトの歴史

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.

### 採用の歴史

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.

### 使われ方

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.

### パッケージ好きにとっての重要性

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.

### タイムライン

- 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.

### ソース

- 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


## セキュリティノート

salmon に一致するローカルシークレット処理マニフェストは見つかりませんでした。将来の対応で安定したパッケージ URL を使えるよう、Nucleus パッケージメタデータはここに公開されています。


## 他のパッケージマネージャ記録

- 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)


## ソース

- pkg.so package database
- curated package history
- pkgdb category and tag curation
- external package-manager database matches
- cross-ecosystem install command graph