# 使用 Homebrew, apt, Nix 安装 spades

查看 spades 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。

## 安装

```sh
sudo av install brew:spades
```

其他安装命令:

### macOS

- Homebrew (100%):

```sh
brew install spades
```

  证据: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install spades
```

  证据: 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
```

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

## 软件包事实

- **软件包键:** brew:spades
- **软件包管理器:** Homebrew
- **软件包管理器页面:** <https://formulae.brew.sh/formula/spades>
- **版本:** 4.3.0
- **来源摘要:** De novo genome sequence assembly
- **主页:** <https://ablab.github.io/spades/>
- **仓库:** <https://github.com/ablab/spades>
- **上游文档:** <https://ablab.github.io/spades>
- **许可证:** GPL-2.0-only
- **源码归档:** <https://github.com/ablab/spades/archive/refs/tags/v4.3.0.tar.gz>
- **最后更新:** 2026-06-14T16:22:41Z
- **已生成:** 2026-07-08T18:08:21+00:00

## 可执行文件

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

## 依赖

- libomp
- python@3.14

## 构建依赖

- cmake

## 安装行为

- post-install 钩子: 未定义
- Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## 版本和新鲜度

- 页面生成时间: 2026-07-08
- 管理器版本: 4.3.0
- 管理器更新时间: 2026-06-14
- 本地数据: OK
- 上游仓库: https://github.com/ablab/spades
- 检测到的最新版本: v4.3.0 (当前)
## 项目历史与用法

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.

### 项目历史

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.

### 采用历史

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.

### 使用方式

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.

### 为什么软件包爱好者会关心

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.

### 时间线

- 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.

### 来源

- <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


## 安全说明

narrow executable package without higher-risk signals.

- **Geiger 风险:** 绿色 / 低
- narrow executable package without higher-risk signals

## 源数据库详情

- **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

## 其他软件包管理器记录

- 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/


## 相关链接

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


## 来源

- 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