# bismark を Homebrew でインストール

bismark 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:bismark
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install bismark
```

  証拠: local Homebrew formula metadata

## パッケージ情報

- **パッケージキー:** brew:bismark
- **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/bismark>
- **バージョン:** 3.1.0
- **ソース概要:** Bisulfite read mapper and methylation caller
- **ホームページ:** <https://github.com/FelixKrueger/Bismark>
- **リポジトリ:** <https://github.com/FelixKrueger/Bismark>
- **ライセンス:** GPL-3.0-only
- **ソースアーカイブ:** <https://github.com/FelixKrueger/Bismark/archive/refs/tags/bismark-rust-v3.1.0.tar.gz>
- **最終更新:** 2026-07-13T18:28:52Z
- **生成日時:** 2026-08-04T22:13:35+00:00

## 実行可能ファイル

- 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 (エイリアス)
- bam2nuc (エイリアス)
- bismark (エイリアス)
- bismark2bedGraph (エイリアス)
- bismark2report (エイリアス)
- bismark2summary (エイリアス)
- bismark_genome_preparation (エイリアス)
- bismark_methylation_extractor (エイリアス)
- coverage2cytosine (エイリアス)
- deduplicate_bismark (エイリアス)
- filter_non_conversion (エイリアス)
- methylation_consistency (エイリアス)

## 依存関係

- bowtie2
- minimap2

## ビルド依存関係

- rust

## インストール挙動

- post-install フック: 未定義
- Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## バージョンと鮮度

- ページ生成日: 2026-08-04
- マネージャ版: 3.1.0
- マネージャ更新日: 2026-07-13
- ローカルデータ: OK
- 上流リポジトリ: https://github.com/FelixKrueger/Bismark
- 情報: No cached GitHub release or tag data was available.
## プロジェクトの歴史と使われ方

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.

### プロジェクトの歴史

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.

### 採用の歴史

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.

### 使われ方

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.

### パッケージ好きにとっての重要性

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.

### タイムライン

- 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.

### ソース

- <https://academic.oup.com/bioinformatics/article/27/11/1571/216956>
- <https://felixkrueger.github.io/Bismark/>
- <https://github.com/FelixKrueger/Bismark>
- <https://www.bioinformatics.babraham.ac.uk/projects/bismark/>
- input.source_facts.package-manager


## セキュリティノート

bismark に一致するローカルシークレット処理マニフェストは見つかりませんでした。将来の対応で安定したパッケージ URL を使えるよう、パッケージメタデータはここに公開されています。


## ソースデータベース詳細

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** bismark
- **Version Scheme:** 0
- **Revision:** 0
- **Head Version:** HEAD
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** head, stable


## 関連リンク

- [Source-control packages](https://pkg.so/ja/source-control-tools/) - Belongs to a source-control command family.
- [Terminal utility packages](https://pkg.so/ja/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://pkg.so/ja/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://pkg.so/ja/scientific-computing-tools/) - Matched scientific computing metadata.
- [minimap2](https://pkg.so/ja/brew/minimap2/) - Runtime dependency declared by Homebrew.
- [bowtie2](https://pkg.so/ja/brew/bowtie2/) - Runtime dependency declared by Homebrew.
- [rust](https://pkg.so/ja/brew/rust/) - Build dependency declared by Homebrew.
- [mosdepth](https://pkg.so/ja/brew/mosdepth/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science, wgs.
- [augustus](https://pkg.so/ja/brew/augustus/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [tabixpp](https://pkg.so/ja/brew/tabixpp/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [chopper](https://pkg.so/ja/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [minigraph](https://pkg.so/ja/brew/minigraph/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [samtools](https://pkg.so/ja/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [blast](https://pkg.so/ja/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [bedtools](https://pkg.so/ja/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
- [mummer](https://pkg.so/ja/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)


## ソース

- 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