macOS
Homebrewvérifié · 100%
brew install jellyfishlocal Homebrew formula metadata
brew
Installer jellyfish avec Homebrew, apt, Nix
Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de jellyfish pour les workflows d'agents IA.
installation
Commandes d'installation supplémentaires
Linux
Debian aptvérifié · 92%
sudo apt install jellyfishDebian stable package indexes · jellyfish · Source: deb.debian.org
Nixvérifié · 92%
nix profile install nixpkgs#jellyfishnixpkgs package indexes · pkgs/by-name/je/jellyfish/package.nix · Source: api.github.com
aperçu
Résumé du paquet
Fast, memory-efficient counting of DNA k-mers
Liens du projet
Commandes et alias
- jellyfish
historique
Historique du projet et usages
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.
Historique du projet
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.
Historique d'adoption
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.
Modes d'utilisation
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.
Pourquoi les passionnés de paquets s'y intéressent
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.
Chronologie
- 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
posture de sécurité
Niveau de risque : vert
narrow executable package without higher-risk signals.
Classificateur de risque
risque vert · confiance faible · appliance
Pourquoi
- narrow executable package without higher-risk signals
Signaux
- metadata:no-higher-risk-signals
Comportement d'installation
- Aucun hook post-install Homebrew n’est enregistré dans les métadonnées de formule.
- Les métadonnées de bottle Homebrew sont disponibles pour 10 plateformes.
- S’installe avec 1 dépendances d’exécution.
- Les métadonnées de compilation listent 1 dépendances de compilation.
Revue recommandée
Avant une utilisation sans surveillance par un agent, vérifiez si l'outil lit des identifiants en clair, écrit un état distant, publie des artefacts ou lance des plugins.
exécutables
Exécutables installés
| Commande | Type | Exposition | Note |
|---|---|---|---|
jellyfish | cli | exécutable global |
fraîcheur
Version et fraîcheur
Ces signaux séparent l'âge de génération de la page, l'activité du gestionnaire de paquets et la comparaison avec les versions amont. Un retard de version n'est signalé que lorsqu'une URL de preuve et des versions comparables sont présentes.
page générée2026-07-10
version du gestionnaire2.3.1
gestionnaire mis à jour2026-06-19
données localesOK
amontnot checked
dernière version détectéenon détecté
https://github.com/gmarcais/Jellyfish
- infoNo cached GitHub release or tag data was available.https://github.com/gmarcais/Jellyfishconfiance none
métadonnées d'installation
Métadonnées du paquet
| Clé du paquet | brew:jellyfish |
|---|---|
| Version | 2.3.1 |
| Gestionnaire de paquets | Homebrew |
| Page du gestionnaire de paquets | https://formulae.brew.sh/formula/jellyfish |
| Page d'accueil | https://github.com/gmarcais/Jellyfish |
| Dépôt | https://github.com/gmarcais/Jellyfish |
| Docs amont | https://github.com/gmarcais/Jellyfish#readme |
| Licence | BSD-3-Clause OR GPL-3.0-or-later |
| Archive source | https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/jellyfish-2.3.1.tar.gz |
| Dernière mise à jour | 2026-06-19T12:31:21-07:00 |
| Pulse | updated |
| Dépendances | htslib |
| Dépendances de compilation | pkgconf |
| Bouteille | disponible (sur arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, x86_64_linux) |
| post-install Homebrew | non défini |
| Service | aucun déclaré |
faits du registre
Détails de la base source
| 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 |
|
correspondances dans les bases sources
Autres enregistrements de gestionnaires de paquets
Les correspondances proviennent d’index externes de gestionnaires de paquets et restent séparées des liens de paquets Automic Vault locaux.
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 Dépendances
- normalized package name match
- Correspondance par : 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 dépendances optionnelles
- normalized package name match
- Correspondance par : 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 Dépendances
- 1 fournit
- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : Jellyfish
Nix95%
jellyfish
nix profile install nixpkgs#jellyfish- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : 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 dépendances optionnelles
- normalized package name match
- Correspondance par : 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 Dépendances
- 1 fournit
- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : 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 Dépendances
- normalized package name match
- Correspondance par : Jellyfish
piste source
Généré depuis les données du dépôt
Cette page est servie par av-web depuis l'artéfact SQLite privé des paquets généré par scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Sources utilisées
- 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