Kraken 2 Databases

As of September 2020, all available Kraken2 indices will be hosted on the following Amazon Web Services site: https://github.com/BenLangmead/aws-indexes. This website will be frequently updated with the most widely used Kraken2 indices.

Kraken 2 Code Download

• Source (99 KB): Kraken2's source code and README. The current official version of Kraken 2 is v2.0.8-beta (released April 25th, 2019). However, additional fixes/changes are in the newest github version.
• The source code for the current release and the newest version are both available at the Kraken 2 GitHub repository.

Pre-built Kraken 2 Databases

These additional databases have been provided by non-CCB labs:

• GTDB_r89_54k linkA collection of database files for use with Centrifuge, Kraken 1, or Kraken 2 that can be used to classify metagenomes using the GTDB_389_54k index. More information and details at: https://github.com/rrwick/Metagenomics-Index-Correction
• Maxikraken2 and Kraken2-microbial databases. These databases are maintained by LomanLab. More information at the link provided.