CCB » Software » Bracken

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.

NOTE: Bracken is compatible with both Kraken 1.0 and Kraken 2.0. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1.0 defaults, specify 31 as the kmer length. If you use Kraken 2.0 defaults, specify 35 as the kmer length.


News

  • 09/10/2018 - v2.0.0 release
    This release provides bracken-build/bracken shell scripts to check for necessary files and execute all Bracken steps. bracken-build is used to generate files for the database while bracken itself performs the abundance estimation for a given sample. The README.md file describes how to run Bracken using EITHER the new shell scripts OR each individual step.

    The Bracken Manual has been updated to describe how to run Bracken using the new shell scripts.
  • 09/07/2018 - kmer2read_distr files to replace count-kmer-abundances.pl
    A new set of C++ scripts is provided in place of the count-kmer-abundances.pl script to provide faster generation of the kmer distribution files needed for each database. All other scripts remain the same. See the github README.md for the updated steps/command lines.
  • 11/1/2017 - Minikraken2017 Bracken files released
    As part of the release Kraken v1.0 and minikraken updates, [see Kraken], we are also releasing a few pre-built kmer distribution files that compatible with the released minikraken databases. See Downloads for download links and details.
  • 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

Publications

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

Downloads and Links

Minikraken Bracken Files Minikraken is a pre-built Kraken database of Refseq bacterial/archaeal/viral genomes. Two updated minikraken databases were released on October 19th, 2017. For more information about minikraken, see Kraken's Website. To allow minikraken users to also analyze their datasets using Bracken, we provide here Bracken kmer distribution files corresponding to the minikraken 4GB and 8GB databases:

As of Sept 10, 2018, MiniKraken is only released for Kraken 1.0.

Licensing Information

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


Authors/Contributors

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

Page Updated: 2018/09/10

Back to top