Centrifuge: rapid and sensitive classification of metagenomic sequences

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 4078 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…

• NS
  National Science Foundation

  Awards: ABI-1356078, R01-HG006677, 1356078
• NI
  National Institutes of Health

  Awards: R01-HG006677, W911NF-1410490, R01-GM083873, HG006677
• AR
  Army Research Office

  Awards: W911NF, W911NF-1410490