The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
ConStrains identifies microbial strains in metagenomic datasets
Open accessAbstract
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.
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Cited by
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Metadata
- Authors
- Luo, C., Knight, R., Siljander, H., Knip, M., Xavier, R. J., & Gevers, D.
- Venue
- Nature Biotechnology
- Published
- 2015-09-07
- Volume
- 33
- Issue
- 10
- Pages
- 1045-1052
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1433995531
- Cited by
- 267
- References
- 37
- FWCI
- 13.25
- Type
- journal article
- Language
- en
- Open access
- green
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