Ocean viruses: Rigorously evaluating the metagenomic sample-to-sequence pipeline

As new environments are studied, viruses consistently emerge as important and prominent players in natural and man-made ecosystems. However, much of what we know is built both upon the foundation of the culturable minority and using methods that are often insufficiently ground-truthed. Here, we review the modern culture-independent viral metagenomic sample-to-sequence pipeline and how next-generation sequencing techniques are drastically altering our ability to systematically and rigorously evaluate them. Together, a series of studies quantitatively evaluate existing and new methods that allow—even for ultra-low DNA samples—the generation of replicable, near-quantitative datasets that maximize inter-comparability and biological inference.

► We introduce viral ecology and call for quantitative rigor in the field. ► We discuss the challenges for quantitatively interpreting marker-based diversity studies. ► We review recent empirical studies that edge us towards quantitative viral metagenomics.