Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline

Small-scale sequencing has improved substantially in recent decades, culminating in the development of next-generation sequencing (NGS) technologies. Modern NGS methods have helped the discovery of many new plant viruses. Nevertheless, there is still a need to establish solid assembly pipelines targeting small genomes characterised by low identities to known viral sequences. Here, we describe and discuss the fundamental steps required for discovering and sequencing new plant viral genomes by NGS. A practical pipeline and standard alternative tools used in NGS analysis are presented.