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.

Assembly, Coverage analysis, K-mer analysis, Metagenomics, Motif discovery, Virus discovery, Viruses, Zoonotic pathogens,
Frontiers in Microbiology
Department of Virology

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