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DESMAN : a new tool for de novo extraction of strains from metagenomes
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Quince, Christopher , Delmont, Tom O., Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E., Collins, Gavin and Eren, A. Murat (2017) DESMAN : a new tool for de novo extraction of strains from metagenomes. Genome Biology, 18 (1). doi:10.1186/s13059-017-1309-9
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Official URL: http://dx.doi.org/10.1186/s13059-017-1309-9
Abstract
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.
| Item Type: | Journal Article | ||||||
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Journal or Publication Title: | Genome Biology | ||||||
| Publisher: | BioMed Central Ltd. | ||||||
| ISSN: | 1474-7596 | ||||||
| Official Date: | 21 September 2017 | ||||||
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| Volume: | 18 | ||||||
| Number: | 1 | ||||||
| DOI: | 10.1186/s13059-017-1309-9 | ||||||
| Status: | Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Access rights to Published version: | Open Access | ||||||
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