Global trade of plant material has increased the introduction of foreign plant viruses in nations across the world. This has led to the need for increased abilities to detect plant viruses. Surveys assessing the viral biodiversity of environments often use Next Generation Sequencing (NGS) as a tool for virus discovery. NGS has yet to be used as a diagnostic tool due to the computational and time requirements of analyzing NGS data. The purpose of this work is first to show the importance of virus discovery, and second to describe the development and validation of a bioinformatic pipeline designed to detect and identify both DNA and RNA viruses by using pathogen-specific probes to detect virus sequence signals in a metagenomic sample dataset. Finally, Chapter VI shows how the bioinformatic pipeline can be used for the detection of unknown viruses by using general probes.