Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

Ladner, Jason T.; Beitzel, Brett; Chain, Patrick S. G.; Davenport, Matthew G.; Donaldson, Eric; Frieman, Matthew; Kugelman, Jeffrey; Kuhn, Jens H.; O’Rear, Jules; Sabeti, Pardis C.; Wentworth, David E.; Wiley, Michael R.; Yu, Guo-Yun; Sozhamannan, Shanmuga; Bradburne, Christopher; Palacios, Gustavo

Despite the small sizes of viral genomes, complications related to limited RNA quantities, host "contamination," and secondary structure mean that it is often not time-or cost-effective to finish every genome, and given the intended use, finishing may be unnecessary (5) . Therefore, we have used technology-agnostic criteria to define five standard categories designed to encompass the levels of completeness most often encountered in viral sequencing projects. Each viral family/species comes with its own challenges (e.g., secondary structure and GC content); therefore, we provide only loose guidance on the depth of sequence coverage likely required to obtain different levels of finishing. In reality, a similar amount of data will generate genomes with different levels of finishing for different viruses.