Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity.
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ABSTRACT:
SUBMITTER: Brown CT
PROVIDER: S-EPMC7336657 | biostudies-literature | 2020 Jul
REPOSITORIES: biostudies-literature
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Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity.
Brown C Titus CT Moritz Dominik D O'Brien Michael P MP Reidl Felix F Reiter Taylor T Sullivan Blair D BD
Genome biology 20200706 1
Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome. We apply this system to recover missing content from genome bins and show that substantial genomic sequence variation is present in a real metagenome ...[more]
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