# 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 ```sh sudo av install brew:jellyfish ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install jellyfish ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install jellyfish ``` Evidence: Debian stable package indexes: jellyfish from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#jellyfish ``` Evidence: nixpkgs package indexes: pkgs/by-name/je/jellyfish/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## Package facts - **Package key:** brew:jellyfish - **Package manager:** Homebrew - **Package manager page:** - **Version:** 2.3.1 - **Source summary:** Fast, memory-efficient counting of DNA k-mers - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** BSD-3-Clause OR GPL-3.0-or-later - **Source archive:** - **Last updated:** 2026-06-19T12:31:21-07:00 - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - jellyfish (cli) - jellyfish (alias) ## Dependencies - htslib ## Build dependencies - pkgconf ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 2.3.1 - Package-manager updated: 2026-06-19 - Local data: ok - Upstream repository: https://github.com/gmarcais/Jellyfish - info: No cached GitHub release or tag data was available. ## 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 - - - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** jellyfish - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - jellyfish - 2.3.1-4+b1: normalized package name match | Debian stable package indexes: jellyfish from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | count k-mers in DNA sequences | https://www.genome.umd.edu/jellyfish.html - Debian apt - jellyfish-examples - 2.3.1-4: normalized package name match | Debian stable package indexes: jellyfish-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | count k-mers in DNA sequences (examples for testing) | https://www.genome.umd.edu/jellyfish.html - Debian apt - libjellyfish-2.0-2 - 2.3.1-4+b1: normalized package name match | Debian stable package indexes: libjellyfish-2.0-2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | count k-mers in DNA sequences (dynamic library of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Debian apt - libjellyfish-2.0-dev - 2.3.1-4+b1: normalized package name match | Debian stable package indexes: libjellyfish-2.0-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | count k-mers in DNA sequences (development files of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Debian apt - libjellyfish-perl - 2.3.1-4+b1: normalized package name match | Debian stable package indexes: libjellyfish-perl from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | count k-mers in DNA sequences (Perl bindings of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Debian apt - python3-dna-jellyfish - 2.3.1-4+b1: normalized package name match | Debian stable package indexes: python3-dna-jellyfish from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | count k-mers in DNA sequences (Python bindings of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Nix - jellyfish: normalized package name match | nixpkgs package indexes: pkgs/by-name/je/jellyfish/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - jellyfish - 2.3.1-3build1: normalized package name match | Ubuntu 24.04 LTS package indexes: jellyfish from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | count k-mers in DNA sequences | https://www.genome.umd.edu/jellyfish.html - Ubuntu apt - jellyfish-examples - 2.3.1-3build1: normalized package name match | Ubuntu 24.04 LTS package indexes: jellyfish-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | count k-mers in DNA sequences (examples for testing) | https://www.genome.umd.edu/jellyfish.html - Ubuntu apt - libjellyfish-2.0-2 - 2.3.1-3build1: normalized package name match | Ubuntu 24.04 LTS package indexes: libjellyfish-2.0-2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | count k-mers in DNA sequences (dynamic library of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Ubuntu apt - libjellyfish-2.0-dev - 2.3.1-3build1: normalized package name match | Ubuntu 24.04 LTS package indexes: libjellyfish-2.0-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | count k-mers in DNA sequences (development files of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Ubuntu apt - libjellyfish-perl - 2.3.1-3build1: normalized package name match | Ubuntu 24.04 LTS package indexes: libjellyfish-perl from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | count k-mers in DNA sequences (Perl bindings of jellyfish) | https://www.genome.umd.edu/jellyfish.html - Ubuntu apt - python3-dna-jellyfish - 2.3.1-3build1: normalized package name match | Ubuntu 24.04 LTS package indexes: python3-dna-jellyfish from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | count k-mers in DNA sequences (Python bindings of jellyfish) | https://www.genome.umd.edu/jellyfish.html ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [htslib](https://www.automicvault.com/pkg/brew/htslib/) - Runtime dependency declared by Homebrew. - [pkgconf](https://www.automicvault.com/pkg/brew/pkgconf/) - Build dependency declared by Homebrew. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [breseq](https://www.automicvault.com/pkg/brew/breseq/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [fastk](https://www.automicvault.com/pkg/brew/fastk/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, k-mer, science. - [lastz](https://www.automicvault.com/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [minimap2](https://www.automicvault.com/pkg/brew/minimap2/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [mummer](https://www.automicvault.com/pkg/brew/mummer/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [abricate](https://www.automicvault.com/pkg/brew/abricate/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [bioperl](https://www.automicvault.com/pkg/brew/bioperl/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science. - [freebayes](https://www.automicvault.com/pkg/brew/freebayes/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, htslib, science. - [stringtie](https://www.automicvault.com/pkg/brew/stringtie/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, htslib, science. ## Combined YAML source View the package source record on GitHub. [combined/jellyfish.yml](https://github.com/automic-vault/db/blob/main/combined/jellyfish.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph