# Installer bismark avec Homebrew Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de bismark pour les workflows d'agents IA. ## installation ```sh sudo av install brew:bismark ``` Commandes d'installation supplémentaires: ### macOS - Homebrew (100%): ```sh brew install bismark ``` Preuve: local Homebrew formula metadata ## Faits du paquet - **Clé du paquet:** brew:bismark - **Gestionnaire de paquets:** Homebrew - **Version:** 3.1.0 - **Résumé source:** Bisulfite read mapper and methylation caller - **Page d'accueil:** - **Dépôt:** - **Dernière mise à jour:** 2026-07-13T18:28:52Z - **Généré:** 2026-08-03T19:37:03+00:00 ## exécutables - 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) ## Comportement d'installation - Bouteille: non disponible ## Version et fraîcheur - page générée: 2026-08-03 - version du gestionnaire: 3.1.0 ## Historique du projet et usages 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. ### Historique du projet 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. ### Historique d'adoption 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. ### Modes d'utilisation 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. ### Pourquoi les passionnés de paquets s'y intéressent 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. ### Chronologie - 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 ## Notes de sécurité Aucun manifest local de gestion des secrets correspondant n'a été trouvé pour bismark. Les métadonnées de paquet Nucleus restent publiées ici afin que la couverture future dispose d'une URL stable. ## 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 - curated package history - pkgdb category and tag curation - cross-ecosystem install command graph