MetaCarvel: linking assembly graph motifs to biological variants

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dc.contributor.authorGhurye, Jay
dc.contributor.authorTreangen, Todd
dc.contributor.authorFedarko, Marcus
dc.contributor.authorHervey, W. Judson IV
dc.contributor.authorPop, Mihai
dc.date.accessioned2021-06-07T15:51:31Z
dc.date.available2021-06-07T15:51:31Z
dc.date.issued2019-08-26
dc.description.abstractReconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains. Previous methods have addressed these issues by smoothing genomic variants. We present a variant-aware metagenomic scaffolder called MetaCarvel, which combines new strategies for repeat detection with graph analytics for the discovery of variants. We show that MetaCarvel can accurately reconstruct genomic segments from complex microbial mixtures and correctly identify and characterize several classes of common genomic variants.en_US
dc.description.urihttps://doi.org/10.1186/s13059-019-1791-3
dc.identifierhttps://doi.org/10.13016/yfrj-f7gw
dc.identifier.citationGhurye, J., Treangen, T., Fedarko, M. et al. MetaCarvel: linking assembly graph motifs to biological variants. Genome Biol 20, 174 (2019).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27118
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectMetagenomicsen_US
dc.subjectVariant detectionen_US
dc.subjectScaffoldingen_US
dc.subjectAssemblyen_US
dc.titleMetaCarvel: linking assembly graph motifs to biological variantsen_US
dc.typeArticleen_US

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