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bioRxiv · 10.1101/054965

Centrifuge: rapid and sensitive classification of metagenomic sequences

Daehwan Kim·Li Song·Florian P Breitwieser·Steven L Salzberg
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Abstract

Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4,078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI non-redundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer based indexing schemes, which require far more extensive space. Centrifuge is available as free, open-source software from www.ccb.jhu.edu/software/centrifuge

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Daehwan Kim, Li Song, Florian P Breitwieser, Steven L Salzberg. 2016-05-24. Centrifuge: rapid and sensitive classification of metagenomic sequences. https://doi.org/10.1101/054965

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