Journal
GENOME BIOLOGY
Volume 15, Issue 3, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/gb-2014-15-3-r46
Keywords
metagenomics; sequence classification; sequence alignment; next-generation sequencing; microbiome
Funding
- National Institutes of Health [R01 HG006677, R01 GM083873]
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG006677] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM083873] Funding Source: NIH RePORTER
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Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.
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