install

Additional install commands

macOS

Homebrewverified · 100%

brew install spades

local Homebrew formula metadata

Linux

Debian aptverified · 92%

sudo apt install spades

Debian stable package indexes · spades · source: deb.debian.org

Nixverified · 92%

nix profile install nixpkgs#spades

nixpkgs 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

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 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 post-install hook is recorded in formula metadata.
Homebrew bottle metadata is available for 6 platform targets.
Installs with 2 runtime dependencies.
Build metadata lists 1 build dependencies.

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

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 generated2026-07-08

manager version4.3.0

manager updated2026-06-14

local dataok

upstreamcurrent

latest detectedv4.3.0

https://github.com/ablab/spades

okNo freshness warnings were generated.

install metadata

Package metadata

Package key	brew:spades
Version	4.3.0
Package manager	Homebrew
Package manager page	https://formulae.brew.sh/formula/spades
Homepage	https://ablab.github.io/spades/
Repository	https://github.com/ablab/spades
Upstream docs	https://ablab.github.io/spades
License	GPL-2.0-only
Source archive	https://github.com/ablab/spades/archive/refs/tags/v4.3.0.tar.gz
Last updated	2026-06-14T16:22:41Z
Pulse	updated
Dependencies	libomp, python@3.14
Build dependencies	cmake
Bottle	available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install	not defined
Service	none declared

registry facts

Source database details

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

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

Debian stable package indexes · deb.debian.org · Debian stable package indexes: spades from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

Nix95%

spades

nix profile install nixpkgs#spades

normalized package name match
Matched by: Spades

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

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

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: spades from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

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.

combined/spades.yml

Used sources

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

Install spades with Homebrew, apt, Nix