Installer jellyfish avec Homebrew

Liens du projet

• Page d'accueil

Commandes et alias

• jellyfish

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