# Install bismark with Homebrew Bisulfite read mapper and methylation caller. Version 3.1.0 via Homebrew; verified 2026-07-13. ## Install ```sh sudo av install brew:bismark ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install bismark ``` Evidence: local Homebrew formula metadata ## Package facts - **Package key:** brew:bismark - **Package manager:** Homebrew - **Package manager page:** - **Version:** 3.1.0 - **Source summary:** Bisulfite read mapper and methylation caller - **Homepage:** - **Repository:** - **License:** GPL-3.0-only - **Source archive:** - **Last updated:** 2026-07-13T18:28:52Z - **Generated:** 2026-08-04T22:13:35+00:00 ## Executables - 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 (alias) - bam2nuc (alias) - bismark (alias) - bismark2bedGraph (alias) - bismark2report (alias) - bismark2summary (alias) - bismark_genome_preparation (alias) - bismark_methylation_extractor (alias) - coverage2cytosine (alias) - deduplicate_bismark (alias) - filter_non_conversion (alias) - methylation_consistency (alias) ## Dependencies - bowtie2 - minimap2 ## Build dependencies - rust ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-08-04 - Package-manager version: 3.1.0 - Package-manager updated: 2026-07-13 - Local data: ok - Upstream repository: https://github.com/FelixKrueger/Bismark - info: No cached GitHub release or tag data was available. ## Project history and usage 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. ### Project history 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. ### Adoption history 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. ### How it is used 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. ### Why package nerds care 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. ### Timeline - 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. ### Sources - - - - - input.source_facts.package-manager ## Security Notes No matching local secret-handling manifest was found for bismark. Package metadata is still published here so future coverage has a stable package URL. ## Source Database Details - **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 ## Related links - [Source-control packages](https://pkg.so/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://pkg.so/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://pkg.so/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://pkg.so/scientific-computing-tools/) - Matched scientific computing metadata. - [minimap2](https://pkg.so/brew/minimap2/) - Runtime dependency declared by Homebrew. - [bowtie2](https://pkg.so/brew/bowtie2/) - Runtime dependency declared by Homebrew. - [rust](https://pkg.so/brew/rust/) - Build dependency declared by Homebrew. - [mosdepth](https://pkg.so/brew/mosdepth/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science, wgs. - [augustus](https://pkg.so/brew/augustus/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [tabixpp](https://pkg.so/brew/tabixpp/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [chopper](https://pkg.so/brew/chopper/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [minigraph](https://pkg.so/brew/minigraph/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [samtools](https://pkg.so/brew/samtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [blast](https://pkg.so/brew/blast/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [bedtools](https://pkg.so/brew/bedtools/) - Shares pkgdb curated category or tags: bioinformatics, cli, genomics, science. - [mummer](https://pkg.so/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) ## Sources - 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