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About Bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species.


  • 1/02/2017 - Bracken paper published
    The Bracken paper is published online in PeerJ Computer Science.
  • 8/17/2016 - v1.0.0 release
    • This release includes GPLv3 license headers and a set of sample data.
    • The updated README explains the sample files and contains instructions on generating sample output.
  • 5/31/2016 - v0.9.5 release
    This release adds another output file to the script. The new output file (with a extension) is in the same style as the Kraken report file, with reads distributed to the desired level.
  • 5/26/2016 - v0.9.4 release
    Allows multi-threading for script.
  • 4/15/2016 - v0.9.0 release
    First public release of Bracken

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Lu J, Breitwieser FP, Thielen P, Salzberg SL. (2017) Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science 3:e104, doi:10.7717/peerj-cs.104

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Downloads and Links

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Licensing Information

Bracken is open source, licensed under GNU General Public License version 3 (GPLv3).

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Jennifer Lu ( jlu26 jhmi edu )
Florian Breitwieser
Steven Salzberg

For technical issues, bug reports, and code contributions, please use Bracken's GitHub repository.
For other questions/concerns regarding Bracken, contact us at: jlu26 jhmi edu

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