macOS
Homebrewverified · 100%
brew install jellyfishlocal Homebrew formula metadata
brew
Install jellyfish with Homebrew, apt, Nix
Fast, memory-efficient counting of DNA k-mers. Version 2.3.1 via Homebrew; verified 2026-06-19.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install jellyfishDebian stable package indexes · jellyfish · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#jellyfishnixpkgs package indexes · pkgs/by-name/je/jellyfish/package.nix · source: api.github.com
overview
Package summary
Fast, memory-efficient counting of DNA k-mers
Project links
Commands and aliases
- jellyfish
history
Project history and usage
Jellyfish is a fast, memory-efficient k-mer counter for DNA sequence data. The project README and University of Maryland page describe it as a command-line tool that counts k-mers with a compact hash table and compare-and-swap-based parallelism.
Project history
Jellyfish originated with Guillaume Marcais and Carl Kingsford's 2011 Bioinformatics paper, which proposed both a new k-mer counting algorithm and its implementation. The README asks researchers to cite that paper and summarizes the design as an order-of-magnitude memory and speed improvement over other k-mer counters.
The University of Maryland project page preserves the version-1 line and notes that Jellyfish 2.0 moved to a new location with enhancements such as support for longer k-mer sizes and better dynamic memory management. The GitHub repository later became the source and release hub for the 2.x codebase.
Adoption history
Jellyfish became a standard packaged bioinformatics utility because k-mer counting is a common preprocessing step in genome assembly, error correction, and sequence analysis. The README documents installation through Debian and Ubuntu apt, Arch AUR, FreeBSD ports, Cygwin or WSL workflows on Windows, and source builds; the batch input also records Homebrew, Debian, Nix, and Ubuntu packages.
How it is used
Typical use runs jellyfish count on FASTA or multi-FASTA input, then uses commands such as dump, stats, histo, merge, and query to inspect or combine the binary count database. The README also documents C++, Python, Ruby, and Perl bindings for reading Jellyfish output in scripts.
Why package nerds care
For package nerds, Jellyfish is significant because it is not merely a helper binary; it packages a cited algorithm as a reusable command-line primitive for bioinformatics pipelines. Its presence in general-purpose package managers makes a research-grade k-mer counter available without each workflow vendoring its own build.
Timeline
- 2011: Bioinformatics paper was first published online on January 7.
- 2011: University of Maryland page documented Jellyfish as a fast, parallel k-mer counter for DNA.
- 2012: Preserved manuals for the 1.1 series document the classic count, merge, dump, stats, histo, and query workflow.
- Version 2.0: University of Maryland page notes longer k-mer support and better dynamic memory management.
- 2.x: GitHub repository became the source, release, documentation, and bindings hub.
Related projects
- Related projects include other k-mer counters and genome-analysis tools, plus Quake-era workflows referenced by the older manual commands qhisto, qdump, and qmerge. The repository also relates to scripting-language bindings through SWIG.
Sources
- https://academic.oup.com/bioinformatics/article/27/6/764/234905
- https://formulae.brew.sh/formula/jellyfish
- https://github.com/gmarcais/Jellyfish
- https://github.com/gmarcais/Jellyfish#readme
- https://github.com/gmarcais/Jellyfish/tree/master/doc
- https://pubmed.ncbi.nlm.nih.gov/21217122/
- https://www.cbcb.umd.edu/software/jellyfish/index.shtml
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 10 platform targets.
- Installs with 1 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 | Note |
|---|---|---|---|
jellyfish | 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 version2.3.1
manager updated2026-06-19
local dataok
upstreamnot checked
latest detectednot detected
https://github.com/gmarcais/Jellyfish
- infoNo cached GitHub release or tag data was available.https://github.com/gmarcais/Jellyfishnone confidence
install metadata
Package metadata
| Package key | brew:jellyfish |
|---|---|
| Version | 2.3.1 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/jellyfish |
| Homepage | https://github.com/gmarcais/Jellyfish |
| Repository | https://github.com/gmarcais/Jellyfish |
| Upstream docs | https://github.com/gmarcais/Jellyfish#readme |
| License | BSD-3-Clause OR GPL-3.0-or-later |
| Source archive | https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/jellyfish-2.3.1.tar.gz |
| Last updated | 2026-06-19T12:31:21-07:00 |
| Pulse | updated |
| Dependencies | htslib |
| Build dependencies | pkgconf |
| Bottle | available (on arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, 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 | jellyfish |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
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%
jellyfish 2.3.1-4+b1
count k-mers in DNA sequences
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish- Section: science
- Architecture: amd64
- Source Package: jellyfish
- 5 dependencies
- normalized package name match
- Matched by: Jellyfish
Debian apt95%
jellyfish-examples 2.3.1-4
count k-mers in DNA sequences (examples for testing)
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish-examples- Section: science
- Architecture: all
- Source Package: jellyfish
- 1 optional deps
- normalized package name match
- Matched by: Jellyfish
Debian apt95%
libjellyfish-2.0-2 2.3.1-4+b1
count k-mers in DNA sequences (dynamic library of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-2- Section: libs
- Architecture: amd64
- Source Package: jellyfish
- 3 dependencies
- 1 provides
- normalized package name match
- Matched by: Jellyfish
Debian apt95%
libjellyfish-2.0-dev 2.3.1-4+b1
count k-mers in DNA sequences (development files of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-dev- Section: libdevel
- Architecture: amd64
- Source Package: jellyfish
- 1 dependencies
- normalized package name match
- Matched by: Jellyfish
Debian apt95%
libjellyfish-perl 2.3.1-4+b1
count k-mers in DNA sequences (Perl bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-perl- Section: perl
- Architecture: amd64
- Source Package: jellyfish
- 4 dependencies
- normalized package name match
- Matched by: Jellyfish
Debian apt95%
python3-dna-jellyfish 2.3.1-4+b1
count k-mers in DNA sequences (Python bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install python3-dna-jellyfish- Section: python
- Architecture: amd64
- Source Package: jellyfish
- 5 dependencies
- normalized package name match
- Matched by: Jellyfish
Nix95%
jellyfish
nix profile install nixpkgs#jellyfish- normalized package name match
- Matched by: Jellyfish
Ubuntu apt95%
jellyfish 2.3.1-3build1
count k-mers in DNA sequences
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish- Section: universe/science
- Architecture: amd64
- 5 dependencies
- normalized package name match
- Matched by: Jellyfish
Ubuntu apt95%
jellyfish-examples 2.3.1-3build1
count k-mers in DNA sequences (examples for testing)
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish-examples- Section: universe/science
- Architecture: all
- Source Package: jellyfish
- 1 optional deps
- normalized package name match
- Matched by: Jellyfish
Ubuntu apt95%
libjellyfish-2.0-2 2.3.1-3build1
count k-mers in DNA sequences (dynamic library of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-2- Section: universe/libs
- Architecture: amd64
- Source Package: jellyfish
- 3 dependencies
- 1 provides
- normalized package name match
- Matched by: Jellyfish
Ubuntu apt95%
libjellyfish-2.0-dev 2.3.1-3build1
count k-mers in DNA sequences (development files of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-dev- Section: universe/libdevel
- Architecture: amd64
- Source Package: jellyfish
- 1 dependencies
- normalized package name match
- Matched by: Jellyfish
Ubuntu apt95%
libjellyfish-perl 2.3.1-3build1
count k-mers in DNA sequences (Perl bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-perl- Section: universe/perl
- Architecture: amd64
- Source Package: jellyfish
- 4 dependencies
- normalized package name match
- Matched by: Jellyfish
Ubuntu apt95%
python3-dna-jellyfish 2.3.1-3build1
count k-mers in DNA sequences (Python bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install python3-dna-jellyfish- Section: universe/python
- Architecture: amd64
- Source Package: jellyfish
- 5 dependencies
- normalized package name match
- Matched by: Jellyfish
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
- 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