Journal
GENOME BIOLOGY
Volume 18, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-017-1309-9
Keywords
Metagenomes; Strain; Niche
Funding
- Medical Research Council fellowship as part of the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) consortium [MR/M50161X/1, MR/L015080/1]
- European Research Council Starting Grant [3C-BIOTECH 261330]
- Frank R. Lillie Research Innovation Award
- MRC [MR/L015080/1] Funding Source: UKRI
- NERC [NE/M011674/1] Funding Source: UKRI
- Medical Research Council [MR/L015080/1, MR/M50161X/1] Funding Source: researchfish
- Natural Environment Research Council [NE/M011674/1] Funding Source: researchfish
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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.
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