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Front Microbiol. 2015 Oct 1;6:1069. doi: 10.3389/fmicb.2015.01069. eCollection 2015.

Recovering full-length viral genomes from metagenomes.

Author information

1
Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands.
2
Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research Bologna, Italy.
3
Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany.
4
Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands.
5
Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany.

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.

KEYWORDS:

assembly; coverage analysis; k-mer analysis; metagenomics; motif discovery; virus discovery; viruses; zoonotic pathogens

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