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Published on: May 31, 2011
MetaCarvel: linking assembly graph motifs to biological variants
Jay Ghurye1,2, Todd Treangen3, Marcus Fedarko1,2
1Department of Computer Science, University of Maryland, College Park, MD, USA.
Abstract:
Reconstructing 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.
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