# jellyfish を Homebrew, apt, Nix でインストール jellyfish のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。 ## インストール ```sh sudo av install brew:jellyfish ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install jellyfish ``` 証拠: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install jellyfish ``` 証拠: 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 ``` 証拠: nixpkgs package indexes: pkgs/by-name/je/jellyfish/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## パッケージ情報 - **パッケージキー:** brew:jellyfish - **パッケージマネージャ:** Homebrew - **バージョン:** 2.3.1 - **ソース概要:** Fast, memory-efficient counting of DNA k-mers - **ホームページ:** - **リポジトリ:** - **最終更新:** 2026-06-19T12:31:21-07:00 - **生成日時:** 2026-08-03T19:37:03+00:00 ## 実行可能ファイル - jellyfish (エイリアス) ## インストール挙動 - Bottle: 利用不可 ## バージョンと鮮度 - ページ生成日: 2026-08-03 - マネージャ版: 2.3.1 ## プロジェクトの歴史と使われ方 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. ### プロジェクトの歴史 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. ### 採用の歴史 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. ### 使われ方 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. ### パッケージ好きにとっての重要性 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. ### タイムライン - 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. ### ソース - - - - - - - ## セキュリティノート narrow executable package without higher-risk signals. - **Geiger リスク:** グリーン / 低 - narrow executable package without higher-risk signals ## 他のパッケージマネージャ記録 - 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 ## Combined YAML source View the package source record on GitHub. [combined/jellyfish.yml](https://github.com/mxcl/pkgdb/blob/main/combined/jellyfish.yml) ## ソース - pkg.so package database - Geiger risk classifier - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph