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.

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Frontiers in Microbiology
Department of Virology

Smits, S., Bodewes, R., Ruiz-Gonzalez, A., Baumgärtner, V., Koopmans, M., D.V.M., Osterhaus, A., & Schürch, A. (2015). Recovering full-length viral genomes from metagenomes. Frontiers in Microbiology (Vol. 6). doi:10.3389/fmicb.2015.01069