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 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length.

Kraken 1's Website
Kraken 2's Website
Kraken 2/Bracken Pre-Built Databases
KrakenTools Website

News

• 10/2022 - Kraken protocol paper published
  The Kraken protocol paper for Kraken 2, Bracken, and KrakenTools is published online in Nature Protocols
• 06/2022 - Bracken Bug Fix
  In order to fix an issue where species/clades were removed if no unique genomes exist, we no longer redistribute reads at the abundance level/below. Only reads at higher taxonomy levels will be redistributed.
• 09/2020 - Kraken/Bracken AWS Site
  As of September 2020, pre-built Kraken 2/Bracken files will only be available at https://benlangmead.github.io/aws-indexes/k2
• 08/07/2019 - v2.5.0 release
  Bracken-build optimized to allow for 30x faster build times with 16 threads and 1 million database sequences.
• 06/10/2019 - v2.1.0 release
  Output of Kraken-style Bracken report file fixed.
• 04/10/2019 - MiniKraken2 Bracken files UPDATE
  From today on, all 100mer, 150mer, and 200mer Bracken files will no longer be linked directly on this page. Instead, Bracken files will be included in the minikraken2 database download found on the Kraken 2 Website
• 11/02/2018 - MiniKraken2 Bracken files released
  As part of the Kraken2 and MiniKraken2 release, we are also releasing pre-built Bracken files that are compatible with MiniKraken2. See Downloads for download links and details.
• 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

On 09/28/2022, the following Nature Protocols paper has been published detailing how Kraken 2, Bracken, and KrakenTools are used for both Microbiome analysis and Pathogen Detection:

Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. (2022) Metagenome analysis using the Kraken software suite.. Nature Protocolsdoi: 10.1038/s41596-022-00738-y

Downloads and Links

• Source (147 KB): Bracken's source code and README. The current version of Bracken is v2.7.0 (released June 2, 2022).
• The source code is also available in a GitHub repository.
• Link to i100 accuracy data :
• Link to skin microbe data

DOWNLOAD UPDATE 04/10/2019: As of 04/10/2019, all Minikraken Bracken files will be included in the minikraken database downloads themselves and will no longer be linked below. For minikraken databases downloaded prior to this date, feel free to continue using these download links

MiniKraken Bracken Files for Kraken 2

Two MiniKraken databases were released on November 2nd, 2018, representing pre-built 8GB Kraken 2 databases:
MiniKraken2_v1_8GB represents Refseq bacteria/archaea/viral libraries
MiniKraken2_v2_8GB represents Refseq bacteria/archaea/viral libraries AND the GRCh38 human genome.
For more information, see Kraken 2's Website. To allow minikraken users to also analyze their datasets using Bracken, we provide here Bracken kmer distribution files corresponding to each MiniKraken2 database.

• MiniKraken2_v1_8GB Files
  • MiniKraken2_v1_8GB 100mer distribution file
  • MiniKraken2_v1_8GB 150mer distribution file
  • MiniKraken2_v1_8GB 200mer distribution file
• MiniKraken2 v2 8GB Files
  • MiniKraken2_v2_8GB 100mer distribution file
  • MiniKraken2_v2_8GB 150mer distribution file
  • MiniKraken2_v2_8GB 200mer distribution file

MiniKraken Bracken Files for Kraken 1 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:

• Minikraken20171019 4GB 100mer distribution file
• Minikraken20171019 8GB 100mer distribution file
• Minikraken20171019 4GB 125mer distribution file
• Minikraken20171019 8GB 125mer distribution file
• Minikraken20171019 4GB 200mer distribution file
• Minikraken20171019 8GB 200mer distribution file
• MiniBracken.tgz: [5.0MB]: Minikraken2017 4GB/8GB 75mers, 100mers, 200mers files
• seqid2taxid.map (11 MB): For Standard Kraken/Minikraken Databases built in October 2017.

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: 2019/08/07

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