Recovering full-length viral genomes from metagenomes

Saskia Smits, Rogier Bodewes, A Ruiz-Gonzalez, W Baumgartner, Marion Koopmans, Ab Osterhaus, Anita Schürch

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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.
Original languageUndefined/Unknown
JournalFrontiers in Microbiology
Publication statusPublished - 2015

Research programs

  • EMC MM-04-27-01

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