dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms have been developed to comprehensively compare large genome sets, but they are not accurate with draft-quality genomes. Here we present dRep, a program that reduces the computational time for pairwise genome comparisons by sequentially applying a fast, inaccurate estimation of genome distance, and a slow, accurate measure of average nucleotide identity. dRep achieves a 28 × increase in speed with perfect recall and precision when benchmarked against previously developed algorithms. We demonstrate the use of dRep…

• NS
  National Science Foundation

  Awards: 1106400, Grant No. DGE 1106400, DGE 1106400
• AP
  Alfred P. Sloan Foundation

  Awards: DGE 1106400, G 2012-10-05
• NI
  National Institutes of Health

  Award: DGE 1106400