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

The "standard draft" category is for whole shotgun genome assemblies with coverage that is low and/or uneven enough to prevent the assembly of a single contig for Õ†1 genome segments. Genomes in this category are likely to result from samples with low viral titers, such as clinical and environmental samples, or to be those containing regions that are difficult to sequence across (e.g., intergenic hairpin regions) (9) . To distinguish standard drafts from targeted amplification of partial viral sequences, standard drafts should contain at least 1 contig for each genomic segment and should be prepared in a manner that allows the possibility of sequencing the vast majority of a virus's genome. To avoid the inclusion of small pieces of genomes as "drafts," there needs to be some type of minimum cutoff for breadth of coverage. Therefore, we suggest that at least a majority (Õ†50%) of the genome be present for a set of sequences to be considered a draft genome.