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About KrakenTools

KrakenTools is a suite of individual scripts designed for use with Kraken, KrakenUniq, Kraken2, and Bracken. These scripts provide users of the above classification/abundance estimation tools additional support primarily for downstream analysis of Kraken/Bracken results. KrakenTools is an ongoing project led by Jennifer Lu, Ph.D. as part of Salzberg Lab.

12/10/2020 Update: We are currently updating this page to provide in-depth examples of the usage of each KrakenTools script. We thank you for your patience. Meanwhile, please refer to the README file in the KrakenTools Github Repository for usage/examples of all scripts.

09/29/2022 Update: KrakenTools has been published in Nature Protocols

General Scripts

  • extracts specific reads that were classified by Kraken at specified taxonomy IDs.
  • converts Kraken report style output to a krona-compatible TEXT files
  • convert Kraken report style output to a mpa (MetaPhlAn)-style TEXT file
  • combines multiple Kraken reports into a single combined report file
  • combines multiple mpa-style files (output from
  • filters Bracken output files to remove/include specified taxonomy IDs
  • creates a single text file containing Kraken-required taxonomy information
  • makes a kraken-style report file from Kraken default output and the file

Diversity Scripts

  • calculates alpha diversity (Shannon's, Berger-Parker's, Simpson's, Inverse Simpson's, Fisher's) from a Bracken output abundance estimation file.
  • calculates Bray-Curtis dissimilarity beta diversity from Kraken, Krona, and Bracken output files.


KrakenTools has been published in Nature Protocols as of September 28, 2022: Metagenome analysis using the Kraken software suite.

In addition, please cite the related Kraken tool used prior to using the KrakenTools scripts:
  1. Kraken,
  2. KrakenUniq,
  3. Kraken2, and/or
  4. Bracken


KrakenTools can be downloaded from the KrakenTools Github Repository.

Link to Download KrakenTools as a Zip folder


Jennifer Lu, Ph.D.
Natalie Rincon, Ph.D. Student

For technical issues, bug reports, and code contributions, please refer to KrakenTools's GitHub repository.

Page Updated: 2022/09/29

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