# spades を Homebrew, apt, Nix でインストール

spades 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:spades
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install spades
```

  証拠: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install spades
```

  証拠: Debian stable package indexes: spades from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

- Nix (92%):

```sh
nix profile install nixpkgs#spades
```

  証拠: nixpkgs package indexes: pkgs/by-name/sp/spades/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:spades
- **パッケージマネージャ:** Homebrew
- **バージョン:** 4.3.0
- **ソース概要:** De novo genome sequence assembly
- **ホームページ:** <https://ablab.github.io/spades/>
- **リポジトリ:** <https://github.com/ablab/spades>
- **最終更新:** 2026-07-29T14:13:07+09:00
- **生成日時:** 2026-08-03T19:37:03+00:00

## 実行可能ファイル

- coronaspades.py (エイリアス)
- metaplasmidspades.py (エイリアス)
- metaspades.py (エイリアス)
- metaviralspades.py (エイリアス)
- plasmidspades.py (エイリアス)
- rnaspades.py (エイリアス)
- rnaviralspades.py (エイリアス)
- spades-bwa (エイリアス)
- spades-convert-bin-to-fasta (エイリアス)
- spades-core (エイリアス)
- spades-corrector-core (エイリアス)
- spades-gbuilder (エイリアス)
- spades-gfa-split (エイリアス)
- spades-gmapper (エイリアス)
- spades-gsimplifier (エイリアス)
- spades-hammer (エイリアス)
- spades-ionhammer (エイリアス)
- spades-kmer-estimating (エイリアス)
- spades-kmercount (エイリアス)
- spades-read-filter (エイリアス)
- spades.py (エイリアス)
- spades_init.py (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: 4.3.0
## プロジェクトの歴史と使われ方

SPAdes is a genome assembly toolkit distributed as command-line pipelines for sequencing data. In package-manager culture it matters less as a package manager itself and more as a scientific CLI with many entry points that system package indexes make easier to install reproducibly.

### プロジェクトの歴史

The SPAdes project traces its cited work back to the 2012 and 2013 SPAdes papers, and the current official repository was created on GitHub in 2016. Its README presents SPAdes as a toolkit for assembly and analysis of sequencing data, primarily Illumina data, with support for IonTorrent and hybrid modes using long reads as supplementary data.

### 採用の歴史

SPAdes accumulated specialized pipelines around common genomics workflows, including metaSPAdes, plasmidSPAdes, metaviralSPAdes, rnaSPAdes, and coronaSPAdes. The official citation guidance lists papers for these modes, reflecting adoption across bacterial, metagenomic, viral, transcriptomic, plasmid, and public-health sequencing use cases.

### 使われ方

Users usually run `spades.py` or one of the mode-specific wrappers with input read files and an output directory, then inspect generated assemblies and logs. The package also ships standalone utilities for k-mer counting, graph operations, sequence-to-graph alignment, and related assembly tasks.

### パッケージ好きにとっての重要性

SPAdes is a good example of why scientific CLIs get packaged broadly: it has compiled code, Python entry points, test commands, large release artifacts, and many subcommands that researchers want to install through Homebrew, Debian/Ubuntu, Nix, or other reproducible environments instead of hand-building each lab machine.

### タイムライン

- 2012: Early SPAdes paper cited by the official project.
- 2013: Additional early SPAdes paper cited by the official project.
- 2016: Current public GitHub repository created.
- 2017: metaSPAdes paper listed in official citation guidance.
- 2022: coronaSPAdes paper listed in official citation guidance.

### Related projects

- Related SPAdes modes and pipelines include metaSPAdes, plasmidSPAdes, metaviralSPAdes, rnaSPAdes, biosyntheticSPAdes, coronaSPAdes, and SPlitteR.

### ソース

- <https://ablab.github.io/spades/>
- <https://ablab.github.io/spades/citation.html>
- <https://api.github.com/repos/ablab/spades>
- <https://github.com/ablab/spades>
- input.source_facts.package-manager


## セキュリティノート

narrow executable package without higher-risk signals.

- **Geiger リスク:** グリーン / 低
- narrow executable package without higher-risk signals

## 他のパッケージマネージャ記録

- Debian apt - spades - 4.0.0+really3.15.5+dfsg-1: normalized package name match | Debian stable package indexes: spades from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | genome assembler for single-cell and isolates data sets | https://github.com/ablab/spades
- Nix - spades: normalized package name match | nixpkgs package indexes: pkgs/by-name/sp/spades/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
- Ubuntu apt - spades - 3.15.5+dfsg-7: normalized package name match | Ubuntu 24.04 LTS package indexes: spades from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | genome assembler for single-cell and isolates data sets | http://cab.spbu.ru/software/spades/


## Combined YAML source

View the package source record on GitHub. [combined/spades.yml](https://github.com/mxcl/pkgdb/blob/main/combined/spades.yml)


## ソース

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