macOS
Homebrew已验证 · 100%
brew install jellyfishlocal Homebrew formula metadata
安装
其他安装命令
Linux
Debian apt已验证 · 92%
sudo apt install jellyfishDebian stable package indexes · jellyfish · 来源: deb.debian.org
Nix已验证 · 92%
nix profile install nixpkgs#jellyfishnixpkgs package indexes · pkgs/by-name/je/jellyfish/package.nix · 来源: api.github.com
概览
软件包摘要
Fast, memory-efficient counting of DNA k-mers
历史
项目历史与用法
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.
项目历史
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.
采用历史
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.
使用方式
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.
为什么软件包爱好者会关心
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.
时间线
- 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.
来源
- 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
安全态势
风险级别：绿色
narrow executable package without higher-risk signals.
风险分类器
绿色 风险 · 低 置信度 · appliance
原因
- narrow executable package without higher-risk signals
信号
- metadata:no-higher-risk-signals
安装行为
- formula 元数据中未记录 Homebrew post-install 钩子。
- Homebrew bottle 元数据适用于 10 个平台目标。
- 安装时包含 1 个运行时依赖。
- 构建元数据列出 1 个构建依赖。
建议审查
在无人值守的代理使用前，请检查该工具是否读取明文凭据、写入远程状态、发布制品或调用插件。
可执行文件
已安装的可执行文件
| 命令 | 类型 | 暴露范围 | 备注 |
|---|---|---|---|
jellyfish | cli | 全局可执行文件 |
新鲜度
版本和新鲜度
这些信号区分页生成时间、软件包管理器活动和上游发布比较。只有存在证据 URL 和可比较版本时，才会提示版本落后。
页面生成时间2026-07-10
管理器版本2.3.1
管理器更新时间2026-06-19
本地数据OK
上游not checked
检测到的最新版本未检测到
https://github.com/gmarcais/Jellyfish
- 信息No cached GitHub release or tag data was available.https://github.com/gmarcais/Jellyfishnone 置信度
安装元数据
软件包元数据
| 软件包键 | brew:jellyfish |
|---|---|
| 版本 | 2.3.1 |
| 软件包管理器 | Homebrew |
| 软件包管理器页面 | https://formulae.brew.sh/formula/jellyfish |
| 主页 | https://github.com/gmarcais/Jellyfish |
| 仓库 | https://github.com/gmarcais/Jellyfish |
| 上游文档 | https://github.com/gmarcais/Jellyfish#readme |
| 许可证 | BSD-3-Clause OR GPL-3.0-or-later |
| 源码归档 | https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/jellyfish-2.3.1.tar.gz |
| 最后更新 | 2026-06-19T12:31:21-07:00 |
| Pulse | updated |
| 依赖 | htslib |
| 构建依赖 | pkgconf |
| Bottle | 可用 (于 arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, x86_64_linux) |
| Homebrew post-install | 未定义 |
| 服务 | 未声明 |
注册表事实
源数据库详情
| 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 |
|
源数据库匹配
其他软件包管理器记录
匹配项来自外部软件包管理器索引，并与本地 Automic Vault 软件包链接分开显示。
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 依赖
- normalized package name match
- 匹配方式：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 可选依赖
- normalized package name match
- 匹配方式：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 依赖
- 1 提供
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：Jellyfish
Nix95%
jellyfish
nix profile install nixpkgs#jellyfish- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：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 可选依赖
- normalized package name match
- 匹配方式：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 依赖
- 1 提供
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：Jellyfish
来源线索
由仓库数据生成
此页面由 av-web 从 scripts/generate-pkg-sqlite.py 生成的私有软件包 SQLite 工件提供。
Combined YAML source
View the package source record on GitHub.
使用的来源
- 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