# 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
- **パッケージマネージャページ:** <https://formulae.brew.sh/formula/spades>
- **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>
- **上流ドキュメント:** <https://ablab.github.io/spades>
- **ライセンス:** GPL-2.0-only
- **ソースアーカイブ:** <https://github.com/ablab/spades/archive/refs/tags/v4.3.0.tar.gz>
- **最終更新:** 2026-06-14T16:22:41Z
- **生成日時:** 2026-07-08T18:08:21+00:00

## 実行可能ファイル

- coronaspades.py (cli)
- metaplasmidspades.py (cli)
- metaspades.py (cli)
- metaviralspades.py (cli)
- plasmidspades.py (cli)
- rnaspades.py (cli)
- rnaviralspades.py (cli)
- spades-bwa (cli)
- spades-convert-bin-to-fasta (cli)
- spades-core (cli)
- spades-corrector-core (cli)
- spades-gbuilder (cli)
- spades-gfa-split (cli)
- spades-gmapper (cli)
- spades-gsimplifier (cli)
- spades-hammer (cli)
- spades-ionhammer (cli)
- spades-kmer-estimating (cli)
- spades-kmercount (cli)
- spades-read-filter (cli)
- spades.py (cli)
- spades_init.py (cli)
- 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)

## 依存関係

- libomp
- python@3.14

## ビルド依存関係

- cmake

## インストール挙動

- post-install フック: 未定義
- Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## バージョンと鮮度

- ページ生成日: 2026-07-08
- マネージャ版: 4.3.0
- マネージャ更新日: 2026-06-14
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/ablab/spades
- 検出された最新: v4.3.0 (最新)
## 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

## ソースデータベース詳細

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** spades
- **Version Scheme:** 0
- **Revision:** 0
- **Head Version:** HEAD
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** head, stable

## 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/


## 関連リンク

- [Source-control packages](https://www.automicvault.com/ja/pkg/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://www.automicvault.com/ja/pkg/scientific-computing-tools/) - Matched scientific computing metadata.
- [python@3.14](https://www.automicvault.com/ja/pkg/brew/python-3-14/) - Runtime dependency declared by Homebrew.
- [cmake](https://www.automicvault.com/ja/pkg/brew/cmake/) - Build dependency declared by Homebrew.
- [abyss](https://www.automicvault.com/ja/pkg/brew/abyss/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
- [flye](https://www.automicvault.com/ja/pkg/brew/flye/) - Shares av.db curated category or tags: bioinformatics, cli, genome-assembly, science.
- [adapterremoval](https://www.automicvault.com/ja/pkg/brew/adapterremoval/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [alevin-fry](https://www.automicvault.com/ja/pkg/brew/alevin-fry/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [bbtools](https://www.automicvault.com/ja/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [bowtie2](https://www.automicvault.com/ja/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [btllib](https://www.automicvault.com/ja/pkg/brew/btllib/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [cutadapt](https://www.automicvault.com/ja/pkg/brew/cutadapt/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequencing.
- [kraken2](https://www.automicvault.com/ja/pkg/brew/kraken2/) - Both packages touch the same language runtime or ecosystem. Shared terms: bioinformatics, cli, libomp, metagenomics, python.

## Combined YAML source

View the package source record on GitHub. [combined/spades.yml](https://github.com/automic-vault/db/blob/main/combined/spades.yml)


## ソース

- Nucleus package database
- Geiger risk classifier
- package-page enrichment
- curated package history
- package version freshness
- av.db category and tag curation
- package relationship graph
- external package-manager database matches
- cross-ecosystem install command graph