Improved metagenomic analysis with Kraken 2

Genome Biol. 2019 Nov 28;20(1):257. doi: 10.1186/s13059-019-1891-0.


Although Kraken's k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.

Keywords: Alignment-free methods; Metagenomics; Metagenomics classification; Microbiome; Minimizers; Probabilistic data structures.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Metagenomics / methods*
  • Software*