# Install spades with Homebrew, apt, Nix

De novo genome sequence assembly. Version 4.3.0 via Homebrew; verified 2026-07-29. Also installable with debian: sudo apt install spades.

## Install

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

Additional install commands:

### macOS

- Homebrew (100%):

```sh
brew install spades
```

  Evidence: local Homebrew formula metadata

### Linux

- Debian apt (92%):

```sh
sudo apt install spades
```

  Evidence: 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
```

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

## Package facts

- **Package key:** brew:spades
- **Package manager:** Homebrew
- **Version:** 4.3.0
- **Source summary:** De novo genome sequence assembly
- **Homepage:** <https://ablab.github.io/spades/>
- **Repository:** <https://github.com/ablab/spades>
- **Last updated:** 2026-07-29T14:13:07+09:00
- **Generated:** 2026-08-03T19:37:03+00:00

## Executables

- 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)

## Install behavior

- Bottle: not available

## Freshness

- Page generated: 2026-08-03
- Package-manager version: 4.3.0
## Project history and usage

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.

### Project history

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.

### Adoption history

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.

### How it is used

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.

### Why package nerds care

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.

### Timeline

- 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


## Security Notes

narrow executable package without higher-risk signals.

- **Geiger risk:** green / low
- narrow executable package without higher-risk signals

## Other Package-Manager Records

- 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)


## Sources

- 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