Journal
GENOME BIOLOGY
Volume 20, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-019-1891-0
Keywords
Metagenomics; Metagenomics classification; Microbiome; Probabilistic data structures; Alignment-free methods; Minimizers
Funding
- NSF [IIS-1349906]
- NIH [R35-GM130151, R01-GM118568]
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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.
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