title: Finding and identifying the viral needle in the metagenomic haystack: trends and challenges.
abstract: Collectively, viruses have the greatest genetic diversity on Earth, occupy extremely varied niches and are likely able to infect all living organisms. Viral infections are an important issue for human health and cause considerable economic losses when agriculturally important crops or husbandry animals are infected. The advent of metagenomics has provided a precious tool to study viruses by sampling them in natural environments and identifying the genomic composition of a sample. However, reaching a clear recognition and taxonomic assignment of the identified viruses has been hampered by the computational difficulty of these problems. In this perspective paper we examine the trends in current research for the identification of viral sequences in a metagenomic sample, pinpoint the intrinsic computational difficulties for the identification of novel viral sequences within metagenomic samples, and suggest possible avenues to overcome them.
authors.affiliation: Bordeaux Bioinformatics Center, Université de Bordeaux Bordeaux, France ; INSERM U1035, Université de Bordeaux Bordeaux, France.
authors.forename: Hayssam
authors.initials: H
authors.lastname: Soueidan
authors.affiliation: Bordeaux Bioinformatics Center, Université de Bordeaux Bordeaux, France ; Centre National de la Recherche Scientifique/Laboratoire Bordelais de Recherche en Informatique, Université de Bordeaux Talence, France.
authors.forename: Louise-Amélie
authors.initials: LA
authors.lastname: Schmitt
authors.affiliation: Institut National de la Recherche Agronomique, UMR 1332 Biologie du Fruit et Pathologie Villenave d'Ornon, France ; UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux Villenave d'Ornon, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Candresse
authors.affiliation: Bordeaux Bioinformatics Center, Université de Bordeaux Bordeaux, France ; Centre National de la Recherche Scientifique/Laboratoire Bordelais de Recherche en Informatique, Université de Bordeaux Talence, France.
authors.forename: Macha
authors.initials: M
authors.lastname: Nikolski
keywords: NGS; host—pathogen interactions; microbial metagenomics; taxonomic assignment; virome