dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
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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.
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The final B. bifidum dataset encompassed 1,351 unique high-quality sequences, including 156 genomes from cultured isolates and 1,195 MAGs.
“After genome quality control and dereplication using CheckM2 and drep [38,39] , the final B. bifidum dataset encompassed 1,351 unique high-quality sequences, including 156 genomes from cultured isolates and 1,195 MAGs [Supplementary Table 1].”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [39]
Dereplication of the dataset was performed using dRep, with a 99.99% threshold to remove genomic redundancy.
“Dereplication of the dataset was performed using dRep, with a 99.99% threshold to remove genomic redundancy [39] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [39]
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- Authors
- Olm, M. R., Brown, C. T., Brooks, B., & Banfield, J. F.
- Affiliations
- University of California, Berkeley (US)
- Corresponding author
- Banfield, Jillian F
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-07-25
- Volume
- 11
- Issue
- 12
- Pages
- 2864-2868
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC5702732
- OpenAlex
- W2736920791
- Cited by
- 3,031
- References
- 21
- Citations by year
- 2026: 641 · 2025: 663 · 2024: 587 · 2023: 399 · 2022: 289 · 2021: 248 · 2020: 129 · 2019: 54 · 2018: 19 · 2017: 2
- FWCI
- 22.89
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- The ISME Journal (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (1106400)
- Alfred P. Sloan Foundation (DGE 1106400, g-2012-10-05)
- National Institutes of Health (DGE 1106400, 5r01ai092531-13)
- National Institute of Allergy and Infectious Diseases (R01-AI092531)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Bacterial Identification and Susceptibility Testing
- Keywords
- comparative genomics, average nucleotide identity, draft genome sequence, metagenome-assembled genomes, genome recovery, microbial genomes, genome clustering
- MeSH terms
- Algorithms, Bacteria, Software, Genome, Bacterial, Metagenome, Metagenomics
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