Kraken: ultrafast metagenomic sequence classification using exact alignments

Genome Biology

Steven L Salzberg¹  Derrick E Wood² 

[1] Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA;Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

关键词: microbiome;    next-generation sequencing;    sequence alignment;    sequence classification;    metagenomics;   

Others  :  863283
DOI  :  10.1186/gb-2014-15-3-r46

 received in 2013-11-17, accepted in 2014-03-03,  发布年份 2014

【 摘 要 】

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/ webcite.

【 授权许可】

   
2014 Wood and Salzberg; licensee BioMed Central Ltd.

【 图 表 】

Fig. 2.

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