# 使用 Homebrew 安装 bismark 查看 bismark 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:bismark ``` 其他安装命令: ### macOS - Homebrew (100%): ```sh brew install bismark ``` 证据: local Homebrew formula metadata ## 软件包事实 - **软件包键:** brew:bismark - **软件包管理器:** Homebrew - **软件包管理器页面:** - **版本:** 3.1.0 - **来源摘要:** Bisulfite read mapper and methylation caller - **主页:** - **仓库:** - **许可证:** GPL-3.0-only - **源码归档:** - **最后更新:** 2026-07-13T18:28:52Z - **已生成:** 2026-08-04T22:13:35+00:00 ## 可执行文件 - NOMe_filtering (cli) - bam2nuc (cli) - bismark (cli) - bismark2bedGraph (cli) - bismark2report (cli) - bismark2summary (cli) - bismark_genome_preparation (cli) - bismark_methylation_extractor (cli) - coverage2cytosine (cli) - deduplicate_bismark (cli) - filter_non_conversion (cli) - methylation_consistency (cli) - NOMe_filtering (别名) - bam2nuc (别名) - bismark (别名) - bismark2bedGraph (别名) - bismark2report (别名) - bismark2summary (别名) - bismark_genome_preparation (别名) - bismark_methylation_extractor (别名) - coverage2cytosine (别名) - deduplicate_bismark (别名) - filter_non_conversion (别名) - methylation_consistency (别名) ## 依赖 - bowtie2 - minimap2 ## 构建依赖 - rust ## 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: 3.1.0 - 管理器更新时间: 2026-07-13 - 本地数据: OK - 上游仓库: https://github.com/FelixKrueger/Bismark - 信息: No cached GitHub release or tag data was available. ## 项目历史与用法 Bismark is a command-line bisulfite sequencing mapper and methylation caller for high-throughput DNA methylation analysis. It maps bisulfite-treated reads to a reference genome and calls cytosine methylation in CpG, CHG, and CHH contexts. ### 项目历史 Bismark was developed by Felix Krueger in the Babraham Bioinformatics group and published in Bioinformatics in 2011 as a flexible aligner and methylation caller for Bisulfite-Seq applications. The official project page describes it as stable GPL software for mapping bisulfite-converted reads and determining cytosine methylation states. The project began as a Perl suite around external aligners such as Bowtie2 and HISAT2. The current official README states that Bismark is now a supported Rust suite, with the original Perl v0.25.x scripts kept as legacy/maintenance-freeze code. ### 采用历史 Bismark became a common package in sequencing pipelines because it combined bisulfite read mapping and methylation calling in one CLI workflow and produced outputs suitable for downstream genome viewers and reports. The official README documents package-oriented installation paths through Bioconda, crates.io, containers, and prebuilt GitHub release binaries, while the Homebrew formula in the input records it as a brew package. ### 使用方式 Typical use prepares bisulfite-converted reference indexes, aligns single-end or paired-end WGBS/RRBS/PBAT reads, optionally deduplicates alignments, and extracts methylation calls and HTML reports. Bismark is used when methylation context matters because its output separates CpG, CHG, and CHH methylation calls rather than treating all cytosines identically. ### 为什么软件包爱好者会关心 Bismark matters to package maintainers because it wraps a historically multi-script bioinformatics workflow with external aligner requirements, and its current Rust transition changes packaging expectations from Perl scripts plus Samtools to a supported single-suite binary model. It is a useful example of a long-lived scientific CLI where package recipes need to track both legacy reproducibility and a new implementation advertised as byte-identical on the default path. ### 时间线 - 2010: Changelog records Bismark v0.2.x releases. - 2011: Bismark paper published in Bioinformatics. - 2019: Babraham project page records v0.22.x releases. - 2026: Official README describes the Rust suite as the supported default and Perl v0.25.x as legacy. ### Related projects - Bowtie2, HISAT2, and minimap2 are supported alignment backends in current official documentation. - SeqMonk is referenced by the official project pages as a genome viewer that can import Bismark output. ### 来源 - - - - - input.source_facts.package-manager ## 安全说明 没有找到 bismark 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:** bismark - **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 - [Source-control packages](https://pkg.so/zh-hans/source-control-tools/) - Belongs to a source-control command family. - [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. - [minimap2](https://pkg.so/zh-hans/brew/minimap2/) - Runtime dependency declared by Homebrew. - [bowtie2](https://pkg.so/zh-hans/brew/bowtie2/) - Runtime dependency declared by Homebrew. - [rust](https://pkg.so/zh-hans/brew/rust/) - Build dependency declared by Homebrew. - [mosdepth](https://pkg.so/zh-hans/brew/mosdepth/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science, wgs. - [augustus](https://pkg.so/zh-hans/brew/augustus/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [tabixpp](https://pkg.so/zh-hans/brew/tabixpp/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [chopper](https://pkg.so/zh-hans/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [minigraph](https://pkg.so/zh-hans/brew/minigraph/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [samtools](https://pkg.so/zh-hans/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [blast](https://pkg.so/zh-hans/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [bedtools](https://pkg.so/zh-hans/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [mummer](https://pkg.so/zh-hans/brew/mummer/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, dna, filter, genome. ## Combined YAML source View the package source record on GitHub. [combined/bismark.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bismark.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