# Installer bracken avec Homebrew

Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de bracken pour les workflows d'agents IA.

## installation

```sh
sudo av install brew:bracken
```

Commandes d'installation supplémentaires:

### macOS

- Homebrew (100%):

```sh
brew install bracken
```

  Preuve: local Homebrew formula metadata

## Faits du paquet

- **Clé du paquet:** brew:bracken
- **Gestionnaire de paquets:** Homebrew
- **Version:** 3.1
- **Résumé source:** Bayesian estimation of species abundance from Kraken output
- **Page d'accueil:** <https://ccb.jhu.edu/software/bracken/>
- **Dépôt:** <https://github.com/jenniferlu717/Bracken>
- **Dernière mise à jour:** 2026-07-13T04:01:12Z
- **Généré:** 2026-08-03T19:37:03+00:00

## exécutables

- bracken (alias)
- bracken-build (alias)

## Comportement d'installation

- Bouteille: non disponible

## Version et fraîcheur

- page générée: 2026-08-03
- version du gestionnaire: 3.1
## Historique du projet et usages

Bracken, short for Bayesian Reestimation of Abundance with Kraken, is a command-line method for estimating species or higher-level taxonomic abundance from Kraken-classified metagenomic reads.

### Historique du projet

Bracken was developed in the Johns Hopkins Center for Computational Biology ecosystem around Kraken. The official CCB page records the first public release in April 2016 and the Bracken paper in PeerJ Computer Science in January 2017.

The project evolved from Python and support scripts into a workflow with `bracken-build` for database preparation and `bracken` for abundance estimation. The CCB news log records the 2018 v2.0.0 release adding shell scripts for the combined workflow and later build-time optimizations.

### Historique d'adoption

Bracken is adopted as a companion to Kraken 1, KrakenUniq, and Kraken 2 because Kraken assigns reads to taxonomy but does not itself estimate species abundance. Bracken re-estimates abundances by using k-mer distribution probabilities derived from the Kraken database.

The 2022 Nature Protocols Kraken suite paper incorporated Bracken into a step-by-step metagenomic workflow for microbiome analysis and pathogen detection, reinforcing its role as part of the standard Kraken command-line toolchain.

### Modes d'utilisation

A typical Bracken run first builds or obtains a Kraken database, generates Bracken database files for a read length with `bracken-build`, classifies samples with Kraken or Kraken 2, creates a Kraken report, and then runs `bracken` or `estimate_abundance.py` to estimate abundance at a target taxonomic rank.

The manual notes that Bracken supports Kraken 1 and Kraken 2 and that users should account for the default k-mer length difference between those classifiers.

### Pourquoi les passionnés de paquets s'y intéressent

Bracken matters to package maintainers because it is a small CLI package that depends operationally on large external Kraken databases and database-specific k-mer distribution files rather than on a self-contained config file.

It is also a packaging example where the executable surface includes both a user-facing abundance command and a build command that prepares data artifacts for downstream runs.

### Chronologie

- 2016: First public Bracken release recorded by the official CCB page.
- 2017: Bracken paper published in PeerJ Computer Science.
- 2018: v2.0.0 release adds `bracken` and `bracken-build` shell-script workflow.
- 2022: Kraken protocol paper including Bracken published in Nature Protocols.
- 2025: GitHub releases list Bracken v3.1 as the latest release.

### Related projects

- Kraken 1, KrakenUniq, Kraken 2, and KrakenTools are the closest related tools in official Bracken documentation.
- Pavian is part of the broader Kraken-suite visualization workflow referenced in the Nature Protocols article.

### Sources

- <https://ccb.jhu.edu/software/bracken/index.shtml>
- <https://ccb.jhu.edu/software/bracken/index.shtml?t=manual>
- <https://github.com/jenniferlu717/Bracken>
- <https://peerj.com/articles/cs-104/>
- <https://www.nature.com/articles/s41596-022-00738-y>
- input.source_facts.package-manager


## Notes de sécurité

Aucun manifest local de gestion des secrets correspondant n'a été trouvé pour bracken. 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/bracken.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bracken.yml)


## Sources

- pkg.so package database
- curated package history
- pkgdb category and tag curation
- cross-ecosystem install command graph