AUTHOR=Smits Saskia L. , Bodewes Rogier , Ruiz-González Aritz , Baumgärtner Wolfgang , Koopmans Marion P. , Osterhaus Albert D. M. E. , Schürch Anita C. 

TITLE=Recovering full-length viral genomes from metagenomes

JOURNAL=Frontiers in Microbiology

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.01069

DOI=10.3389/fmicb.2015.01069

ISSN=1664-302X

ABSTRACT=<p>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.</p>