macOS
Homebrew確認済み · 100%
brew install jellyfishlocal Homebrew formula metadata
brew
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
追加のインストールコマンド
Linux
Debian apt確認済み · 92%
sudo apt install jellyfishDebian stable package indexes · jellyfish · ソース: deb.debian.org
Nix確認済み · 92%
nix profile install nixpkgs#jellyfishnixpkgs package indexes · pkgs/by-name/je/jellyfish/package.nix · ソース: api.github.com
概要
パッケージ概要
Fast, memory-efficient counting of DNA k-mers
プロジェクトリンク
コマンドとエイリアス
- jellyfish
履歴
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
- 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
セキュリティ状態
リスクレベル: グリーン
narrow executable package without higher-risk signals.
リスク分類器
リスク グリーン · 信頼度 低 · appliance
理由
- narrow executable package without higher-risk signals
信号
- metadata:no-higher-risk-signals
インストール挙動
- formula メタデータに Homebrew post-install フックは記録されていません。
- Homebrew bottle メタデータは 10 個のプラットフォームターゲットで利用できます。
- 1 件の実行時依存関係とともにインストールされます。
- ビルドメタデータには 1 件のビルド依存関係があります。
推奨レビュー
エージェントに無人実行させる前に、このツールが平文の認証情報を読むか、リモート状態を書き込むか、成果物を公開するか、プラグインを起動するかを確認してください。
実行可能ファイル
インストールされる実行可能ファイル
| コマンド | 種類 | 公開範囲 | メモ |
|---|---|---|---|
jellyfish | cli | グローバル実行可能ファイル |
鮮度
バージョンと鮮度
これらの信号は、ページ生成時期、パッケージマネージャの活動、上流リリース比較を分けて示します。バージョン遅れは、証拠 URL と比較可能なバージョンがある場合だけ警告されます。
ページ生成日2026-07-10
マネージャ版2.3.1
マネージャ更新日2026-06-19
ローカルデータOK
上流not checked
検出された最新未検出
https://github.com/gmarcais/Jellyfish
- 情報No cached GitHub release or tag data was available.https://github.com/gmarcais/Jellyfish信頼度 none
インストールメタデータ
パッケージメタデータ
| パッケージキー | brew:jellyfish |
|---|---|
| バージョン | 2.3.1 |
| パッケージマネージャ | Homebrew |
| パッケージマネージャページ | https://formulae.brew.sh/formula/jellyfish |
| ホームページ | https://github.com/gmarcais/Jellyfish |
| リポジトリ | https://github.com/gmarcais/Jellyfish |
| 上流ドキュメント | https://github.com/gmarcais/Jellyfish#readme |
| ライセンス | BSD-3-Clause OR GPL-3.0-or-later |
| ソースアーカイブ | https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/jellyfish-2.3.1.tar.gz |
| 最終更新 | 2026-06-19T12:31:21-07:00 |
| Pulse | updated |
| 依存関係 | htslib |
| ビルド依存関係 | pkgconf |
| Bottle | 利用可能 (対象 arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, x86_64_linux) |
| Homebrew post-install | 未定義 |
| サービス | 宣言なし |
レジストリ情報
ソースデータベース詳細
| 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 |
|
ソースデータベース一致
他のパッケージマネージャ記録
一致は外部パッケージマネージャインデックスから取得され、ローカルの Automic Vault パッケージリンクとは分けて表示されます。
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 依存関係
- normalized package name match
- 一致条件: 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 任意依存関係
- normalized package name match
- 一致条件: 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 依存関係
- 1 提供
- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: Jellyfish
Nix95%
jellyfish
nix profile install nixpkgs#jellyfish- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: 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 任意依存関係
- normalized package name match
- 一致条件: 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 依存関係
- 1 提供
- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: 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 依存関係
- normalized package name match
- 一致条件: Jellyfish
ソース経路
リポジトリデータから生成
このページは scripts/generate-pkg-sqlite.py が生成した非公開のパッケージ SQLite アーティファクトから av-web によって提供されます。
Combined YAML source
View the package source record on GitHub.
使用ソース
- 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