# Installer spades avec Homebrew, apt, Nix

Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de spades pour les workflows d'agents IA.

## installation

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

Commandes d'installation supplémentaires:

### macOS

- Homebrew (100%):

```sh
brew install spades
```

  Preuve: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install spades
```

  Preuve: 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
```

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

## Faits du paquet

- **Clé du paquet:** brew:spades
- **Gestionnaire de paquets:** Homebrew
- **Page du gestionnaire de paquets:** <https://formulae.brew.sh/formula/spades>
- **Version:** 4.3.0
- **Résumé source:** De novo genome sequence assembly
- **Page d'accueil:** <https://ablab.github.io/spades/>
- **Dépôt:** <https://github.com/ablab/spades>
- **Docs amont:** <https://ablab.github.io/spades>
- **Licence:** GPL-2.0-only
- **Archive source:** <https://github.com/ablab/spades/archive/refs/tags/v4.3.0.tar.gz>
- **Dernière mise à jour:** 2026-06-14T16:22:41Z
- **Généré:** 2026-07-08T18:08:21+00:00

## exécutables

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

## Dépendances

- libomp
- python@3.14

## Dépendances de compilation

- cmake

## Comportement d'installation

- hook post-installation: non défini
- Bouteille: disponible sur arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## Version et fraîcheur

- page générée: 2026-07-08
- version du gestionnaire: 4.3.0
- gestionnaire mis à jour: 2026-06-14
- données locales: OK
- dépôt amont: https://github.com/ablab/spades
- dernière version détectée: v4.3.0 (à jour)
## Historique du projet et usages

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.

### Historique du projet

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.

### Historique d'adoption

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.

### Modes d'utilisation

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.

### Pourquoi les passionnés de paquets s'y intéressent

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.

### Chronologie

- 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.

### Sources

- <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


## Notes de sécurité

narrow executable package without higher-risk signals.

- **Risque Geiger:** vert / faible
- narrow executable package without higher-risk signals

## Détails de la base source

- **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

## Autres enregistrements de gestionnaires de paquets

- 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/


## Liens liés

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


## Sources

- 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