biostudies-literatureWood DEDirectorate for Computer and Information Science and EngineeringNational Institute of General Medical SciencesNIGMS NIH HHS257https://www.ebi.ac.uk/biostudies/studies/S-EPMC6883579biostudies-literatureUnknown20(1)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.Genome biologyImproved metagenomic analysis with Kraken 2.PMC6883579R01 GM118568IIS-1349906R01-GM118568R35-GM130151Langmead BWood DELu JfalseImproved metagenomic analysis with Kraken 2.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.2019-01-01T00:00:00Z2019 Nov2026-05-01T10:31:56.345Z2020-05-21T21:08:08ZS-EPMC68835793177966810.1186/s13059-019-1891-0