Install bismark with Homebrew

Project links

• Homepage
• Package manager page

Commands and aliases

• NOMe_filtering
• bam2nuc
• bismark
• bismark2bedGraph
• bismark2report
• bismark2summary
• bismark_genome_preparation
• bismark_methylation_extractor
• coverage2cytosine
• deduplicate_bismark
• filter_non_conversion
• methylation_consistency

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

• 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