Standards for sequencing viral genomes in the era of high-throughput sequencing

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

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

Abstract

Thanks to high-throughput sequencing technologies, genome sequencing has become a common component in nearly all aspects of viral research; thus, we are experiencing an explosion in both the number of available genome sequences and the number of institutions producing such data. However, there are currently no common standards used to convey the quality, and therefore utility, of these various genome sequences. Here, we propose five "standard" categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing. We also provide genome finishing recommendations for various downstream applications, keeping in mind the cost-benefit tradeoffs associated with different levels of finishing. Our goal is to define a common vocabulary that will allow comparison of genome quality across different research groups, sequencing platforms, and assembly techniques.

Original languageEnglish (US)
Article numbere01360-14
Pages (from-to)1-5
Number of pages5
JournalmBio
Volume5
Issue number3
DOIs
StatePublished - Jun 17 2014
Externally publishedYes

ASJC Scopus subject areas

  • Microbiology
  • Virology

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