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Install bismark with Homebrew
Bisulfite read mapper and methylation caller. Version 3.1.0 via Homebrew; verified 2026-07-13.
install
Additional install commands
overview
Package summary
Bisulfite read mapper and methylation caller
Project links
Commands and aliases
- NOMe_filtering
- bam2nuc
- bismark
- bismark2bedGraph
- bismark2report
- bismark2summary
- bismark_genome_preparation
- bismark_methylation_extractor
- coverage2cytosine
- deduplicate_bismark
- filter_non_conversion
- methylation_consistency
history
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
security posture
No protected-tool coverage found yet
No matching local secret-handling manifest was found for bismark. Nucleus package metadata is still published here so future coverage has a stable package URL.
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
NOMe_filtering | executable | indexed executable | Discovered from the local executable index. |
bam2nuc | executable | indexed executable | Discovered from the local executable index. |
bismark | executable | indexed executable | Discovered from the local executable index. |
bismark2bedGraph | executable | indexed executable | Discovered from the local executable index. |
bismark2report | executable | indexed executable | Discovered from the local executable index. |
bismark2summary | executable | indexed executable | Discovered from the local executable index. |
bismark_genome_preparation | executable | indexed executable | Discovered from the local executable index. |
bismark_methylation_extractor | executable | indexed executable | Discovered from the local executable index. |
coverage2cytosine | executable | indexed executable | Discovered from the local executable index. |
deduplicate_bismark | executable | indexed executable | Discovered from the local executable index. |
filter_non_conversion | executable | indexed executable | Discovered from the local executable index. |
methylation_consistency | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version3.1.0
manager updated2026-07-13
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:bismark |
|---|---|
| Version | 3.1.0 |
| Package manager | Homebrew |
| Homepage | https://github.com/FelixKrueger/Bismark |
| Repository | https://github.com/FelixKrueger/Bismark |
| Last updated | 2026-07-13T18:28:52Z |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- cross-ecosystem install command graph
- curated package history
- pkg.so package database
- pkgdb category and tag curation