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DESMAN: a new tool for de novo extraction of strains from metagenomes
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2017 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 18, 181Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD , 2017. Vol. 18, 181
Keyword [en]
Metagenomes, Strain, Niche
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Genetics
Identifiers
URN: urn:nbn:se:kth:diva-215449DOI: 10.1186/s13059-017-1309-9ISI: 000411360100001PubMedID: 28934976Scopus ID: 2-s2.0-85029760699OAI: oai:DiVA.org:kth-215449DiVA: diva2:1150600
Note

QC 20171019

Available from: 2017-10-19 Created: 2017-10-19 Last updated: 2017-10-19Bibliographically approved

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Alneberg, Johannes

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Gene TechnologyScience for Life Laboratory, SciLifeLab
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