macOS
Homebrewverified · 100%
brew install spadeslocal Homebrew formula metadata
brew / rank 5402
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
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install spadesDebian stable package indexes · spades · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#spadesnixpkgs package indexes · pkgs/by-name/sp/spades/package.nix · source: api.github.com
overview
Package summary
De novo genome sequence assembly
Project links
Commands and aliases
- coronaspades.py
- metaplasmidspades.py
- metaspades.py
- metaviralspades.py
- plasmidspades.py
- rnaspades.py
- rnaviralspades.py
- spades-bwa
- spades-convert-bin-to-fasta
- spades-core
- spades-corrector-core
- spades-gbuilder
- spades-gfa-split
- spades-gmapper
- spades-gsimplifier
- spades-hammer
- spades-ionhammer
- spades-kmer-estimating
- spades-kmercount
- spades-read-filter
- spades.py
- spades_init.py
history
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
security posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
coronaspades.py | executable | indexed executable | Discovered from the local executable index. |
metaplasmidspades.py | executable | indexed executable | Discovered from the local executable index. |
metaspades.py | executable | indexed executable | Discovered from the local executable index. |
metaviralspades.py | executable | indexed executable | Discovered from the local executable index. |
plasmidspades.py | executable | indexed executable | Discovered from the local executable index. |
rnaspades.py | executable | indexed executable | Discovered from the local executable index. |
rnaviralspades.py | executable | indexed executable | Discovered from the local executable index. |
spades-bwa | executable | indexed executable | Discovered from the local executable index. |
spades-convert-bin-to-fasta | executable | indexed executable | Discovered from the local executable index. |
spades-core | executable | indexed executable | Discovered from the local executable index. |
spades-corrector-core | executable | indexed executable | Discovered from the local executable index. |
spades-gbuilder | executable | indexed executable | Discovered from the local executable index. |
spades-gfa-split | executable | indexed executable | Discovered from the local executable index. |
spades-gmapper | executable | indexed executable | Discovered from the local executable index. |
spades-gsimplifier | executable | indexed executable | Discovered from the local executable index. |
spades-hammer | executable | indexed executable | Discovered from the local executable index. |
spades-ionhammer | executable | indexed executable | Discovered from the local executable index. |
spades-kmer-estimating | executable | indexed executable | Discovered from the local executable index. |
spades-kmercount | executable | indexed executable | Discovered from the local executable index. |
spades-read-filter | executable | indexed executable | Discovered from the local executable index. |
spades.py | executable | indexed executable | Discovered from the local executable index. |
spades_init.py | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version4.3.0
manager updated2026-07-29
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:spades |
|---|---|
| Version | 4.3.0 |
| Package manager | Homebrew |
| Homepage | https://ablab.github.io/spades/ |
| Repository | https://github.com/ablab/spades |
| Last updated | 2026-07-29T14:13:07+09:00 |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
spades 4.0.0+really3.15.5+dfsg-1
genome assembler for single-cell and isolates data sets
https://github.com/ablab/spades
sudo apt install spades- Section: science
- Architecture: amd64
- 14 dependencies
- normalized package name match
- Matched by: Spades
Nix95%
spades
nix profile install nixpkgs#spades- normalized package name match
- Matched by: Spades
Ubuntu apt95%
spades 3.15.5+dfsg-7
genome assembler for single-cell and isolates data sets
http://cab.spbu.ru/software/spades/
sudo apt install spades- Section: universe/science
- Architecture: amd64
- 14 dependencies
- normalized package name match
- Matched by: Spades
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation