The second version of the Kraken taxonomic sequence classification system

Please refer to the Operating Manual (in docs/MANUAL.html) for details on how to use Kraken 2.

For additional implementation details and guidance on using Kraken 2, you can also refer to:

• The paper describing the first version of Kraken. Note that Kraken 2 is a rewrite of Kraken 1 and is not backwards compatible with Kraken 1.
• The paper describing KrakenUniq. KrakenUniq's HLL-based functionality is incorporated in Kraken 2 when using the --report-minimizer-data flag described in the Operating Manual.
• The Kraken 2 paper.
• A protocol paper describing use of Kraken 2.