Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses

Viral metagenomics is one of the most widely used approaches to study viral population genomics. With the recent development of bioinformatic tools, the number of molecular biological methods, programs, and software to analyze viral metagenome data have greatly increased. Here, we describe the basic analysis workflow along with bioinformatic tools that can be used to analyze viral metagenome data. Although this chapter assumes that the viral metagenome data are prepared from the freshwater samples and are subjected to dsDNA sequencing, the protocol can be applied and modified for other types of metagenome data collected from a variety of sources.