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Recovering full-length viral genomes from metagenomes.

ABSTRACT: Infectious disease metagenomics is driven by the question: "what is causing the disease?" in contrast to classical metagenome studies which are guided by "what is out there?" In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.

SUBMITTER: Smits SL

PROVIDER: S-EPMC4589665 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Recovering full-length viral genomes from metagenomes.

Smits Saskia L SL Bodewes Rogier R Ruiz-González Aritz A Baumgärtner Wolfgang W Koopmans Marion P MP Osterhaus Albert D M E AD Schürch Anita C AC

Frontiers in microbiology 20151001

Infectious disease metagenomics is driven by the question: "what is causing the disease?" in contrast to classical metagenome studies which are guided by "what is out there?" In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment l ...[more]

PMID: 26483782

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