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

In addition to standardizing the vocabulary of viral genome assemblies, it is also critical for researchers to routinely provide raw sequencing reads. Without these, it is impossible for others to independently verify the quality of an assembly. Data repositories such as GenBank already provide a platform for depositing HT sequencing reads, but this is not a requirement for the submission of a genome, nor is this option typically utilized. Wider analysis of data will ultimately result in higher-quality assemblies. It is worth considering broader implementation of a wiki-like, crowdsourcing strategy to genome assembly, similar to the annotation strategies that have been adopted for specific genomes of high interest (23, 24) . This approach would allow multiple parties to work on genome assembly and annotation at the same time and would provide instant updates for the entire community to evaluate and utilize in their own research.