The second version of the Kraken taxonomic sequence classification system
C++
942
360 commits
updated Oct 1, 2026
README
Kraken 2
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.
Publications
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-dataflag described in the Operating Manual. - The Kraken 2 paper.
- A protocol paper describing use of Kraken 2.
Significant stargazers
39 followers · starred Aug 2018
17 followers · starred Apr 2019
116 followers · starred Sep 2019
146 followers · starred Mar 2025
Similar repos
The second version of the Kraken taxonomic sequence classification system
C++
942
360 commits
updated Oct 1, 2026
README
Kraken 2
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.
Publications
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-dataflag described in the Operating Manual. - The Kraken 2 paper.
- A protocol paper describing use of Kraken 2.
Significant stargazers
39 followers · starred Aug 2018
17 followers · starred Apr 2019
116 followers · starred Sep 2019
146 followers · starred Mar 2025