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 est_abundance.py script. The new output file (with a _bracken.report 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 count-kmer-abundances.pl script.
- 4/15/2016 - v0.9.0 release
First public release of Bracken
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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- Source (60 KB): Bracken's source code and README. The current version of Bracken is v1.0.0 (released August 17th, 2016).
- The source code is also available in a GitHub repository.
- Link to i100 accuracy data :
- Link to skin microbe data
Bracken is open source, licensed under GNU General Public License version 3 (GPLv3).