Peer-Reviewed Journal Details
Mandatory Fields
Quince, C,Delmont, TO,Raguideau, S,Alneberg, J,Darling, AE,Collins, G,Eren, AM
2017
September
Genome Biol
DESMAN: a new tool for de novo extraction of strains from metagenomes
Published
Altmetric: 205WOS: 17 ()
Optional Fields
Metagenomes Strain Niche SEQUENCING DATA BACTERIA FACTORIZATION TRANSFORM DISCOVERY ALIGNMENT COVERAGE GENOMICS RARE
18
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.
10.1186/s13059-017-1309-9
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