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

Abstract

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 for genome recovery from time-series datasets. Each metagenome was assembled separately, and dRep was used to identify groups of essentially identical genomes and select the best genome from each replicate set. This resulted in recovery of significantly more and higher-quality genomes compared to the set recovered using co-assembly.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical spongeIanthella basta

“…Trimmed reads from each dataset were assembled using Spades version 3.11.0 (Bankevich et al, 2012), using default parameters and genomes were binned using Metabat v 2.12.0 (Kang et al, 2015). MAGs from multiple Illumina data sets were dereplicated using dRep (Olm et al, 2017) and provisionally classified using CheckM (Parks et al, 2015). A single high-quality archaeal MAG was recovered after dereplication and uploaded to MaGe (Vallenet et al, 2009) for annotation.…”

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

“…Contig sequences were aligned to raw data using BWA (Li & Durbin, 2009) and placed into taxonomic bins with MetaBat2 (Kang, Froula, Egan, & Wang, 2015) using a minimum contig length of 2,000 bp. The comparison and dereplication of recovered genomes bins were completed using dRep (Olm, Brown, Brooks, & Banfield, 2017) with minimum primary Average Nucleotide Identity (ANI) 60% (Varghese et al, 2015) and minimum secondary ANI 95% (Jain, Rodriguez-R, Phillippy, Konstantinidis, & Aluru, 2018). CheckM (Parks, Imelfort, Skennerton, Hugenholtz, & Tyson, 2015) was used to determine completeness and contamination of the best genomes selected by dRep analysis.…”

Taxonomically and metabolically distinct microbial communities with depth and across a hillslope to riparian zone transect

“…Genome abundance across samples -To determine the presence and abundance of genomes across samples, reads from each sample were mapped against genomes with bowtie2 [63]. The average coverage and breadth of coverage of each genome in each sample was then calculated (Olm et al, 2017). Each genome is considered to be present in at least one sample (at a minimum, the sample from which it was originally binned) but could be falsely identified in other samples due to a low breadth cutoff (i.e., false positive).…”

“…Strains detection -Strains of the same species were identified as either genome that shares more than 99% ANI according to their dRep cluster placement [60], or by having an average breadth > 0.99 within more than one sample.…”