# 使用 Homebrew 安装 bracken 查看 bracken 的安装路径、可执行文件、元数据以及面向 AI 代理工作流的安全说明。 ## 安装 ```sh sudo av install brew:bracken ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install bracken ``` 证据: local Homebrew formula metadata ## 软件包事实 - **软件包键:** brew:bracken - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 3.1 - **来源摘要:** Bayesian estimation of species abundance from Kraken output - **主页:** - **仓库:** - **上游文档:** - **许可证:** GPL-3.0-or-later - **源码归档:** - **最后更新:** 2026-07-13T04:01:12Z - **已生成:** 2026-08-04T22:13:35+00:00 ## 可执行文件 - bracken (cli) - bracken-build (cli) - bracken (别名) - bracken-build (别名) ## 依赖 - kraken2 - libomp ## macOS 提供的库 - python ## 安装行为 - post-install 钩子: 未定义 - Bottle: 可用 于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## 版本和新鲜度 - 页面生成时间: 2026-08-04 - 管理器版本: 3.1 - 管理器更新时间: 2026-07-13 - 本地数据: OK - 上游仓库: https://github.com/jenniferlu717/Bracken - 检测到的最新版本: v3.1 (当前) ## 项目历史与用法 Bracken, short for Bayesian Reestimation of Abundance with Kraken, is a command-line method for estimating species or higher-level taxonomic abundance from Kraken-classified metagenomic reads. ### 项目历史 Bracken was developed in the Johns Hopkins Center for Computational Biology ecosystem around Kraken. The official CCB page records the first public release in April 2016 and the Bracken paper in PeerJ Computer Science in January 2017. The project evolved from Python and support scripts into a workflow with `bracken-build` for database preparation and `bracken` for abundance estimation. The CCB news log records the 2018 v2.0.0 release adding shell scripts for the combined workflow and later build-time optimizations. ### 采用历史 Bracken is adopted as a companion to Kraken 1, KrakenUniq, and Kraken 2 because Kraken assigns reads to taxonomy but does not itself estimate species abundance. Bracken re-estimates abundances by using k-mer distribution probabilities derived from the Kraken database. The 2022 Nature Protocols Kraken suite paper incorporated Bracken into a step-by-step metagenomic workflow for microbiome analysis and pathogen detection, reinforcing its role as part of the standard Kraken command-line toolchain. ### 使用方式 A typical Bracken run first builds or obtains a Kraken database, generates Bracken database files for a read length with `bracken-build`, classifies samples with Kraken or Kraken 2, creates a Kraken report, and then runs `bracken` or `estimate_abundance.py` to estimate abundance at a target taxonomic rank. The manual notes that Bracken supports Kraken 1 and Kraken 2 and that users should account for the default k-mer length difference between those classifiers. ### 为什么软件包爱好者会关心 Bracken matters to package maintainers because it is a small CLI package that depends operationally on large external Kraken databases and database-specific k-mer distribution files rather than on a self-contained config file. It is also a packaging example where the executable surface includes both a user-facing abundance command and a build command that prepares data artifacts for downstream runs. ### 时间线 - 2016: First public Bracken release recorded by the official CCB page. - 2017: Bracken paper published in PeerJ Computer Science. - 2018: v2.0.0 release adds `bracken` and `bracken-build` shell-script workflow. - 2022: Kraken protocol paper including Bracken published in Nature Protocols. - 2025: GitHub releases list Bracken v3.1 as the latest release. ### Related projects - Kraken 1, KrakenUniq, Kraken 2, and KrakenTools are the closest related tools in official Bracken documentation. - Pavian is part of the broader Kraken-suite visualization workflow referenced in the Nature Protocols article. ### 来源 - - - - - - input.source_facts.package-manager ## 安全说明 没有找到 bracken 的匹配本地密钥处理 manifest。软件包元数据仍在此发布，以便未来覆盖拥有稳定的软件包 URL。 ## 源数据库详情 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** bracken - **Version Scheme:** 0 - **Revision:** 0 - **Head Version:** HEAD - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** head, stable ## 相关链接 - [Terminal utility packages](https://pkg.so/zh-hans/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://pkg.so/zh-hans/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://pkg.so/zh-hans/scientific-computing-tools/) - Matched scientific computing metadata. - [Homebrew utility packages](https://pkg.so/zh-hans/brew-utility-packages/) - Matched Homebrew package provider. - [kraken2](https://pkg.so/zh-hans/brew/kraken2/) - Runtime dependency declared by Homebrew. - [mmseqs2](https://pkg.so/zh-hans/brew/mmseqs2/) - Shares pkgdb curated category or tags: bioinformatics, cli, metagenomics, science. - [skani](https://pkg.so/zh-hans/brew/skani/) - Shares pkgdb curated category or tags: bioinformatics, cli, metagenomics, science. - [samtools](https://pkg.so/zh-hans/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [blast](https://pkg.so/zh-hans/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [bcftools](https://pkg.so/zh-hans/brew/bcftools/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [seqkit](https://pkg.so/zh-hans/brew/seqkit/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [fastqc](https://pkg.so/zh-hans/brew/fastqc/) - Shares pkgdb curated category or tags: bioinformatics, cli, science. - [abyss](https://pkg.so/zh-hans/brew/abyss/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, libomp, science. ## Combined YAML source View the package source record on GitHub. [combined/bracken.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bracken.yml) ## 来源 - pkg.so package database - package-page enrichment - curated package history - package version freshness - pkgdb category and tag curation - package relationship graph - cross-ecosystem install command graph