CCB » Software » KrakenTools

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.

Current 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


Currently, there is no specific KrakenTools publication. However, as these tools are designed for use with
  1. Kraken,
  2. KrakenUniq,
  3. Kraken2, and/or
  4. Bracken
please cite the relevant tool (refer to links above)


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: 2020/12/10

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