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

Author:

Ladner Jason T.1,Beitzel Brett1,Chain Patrick S. G.2,Davenport Matthew G.3,Donaldson Eric45,Frieman Matthew6,Kugelman Jeffrey1,Kuhn Jens H.57,O’Rear Jules45,Sabeti Pardis C.89,Wentworth David E.10,Wiley Michael R.1,Yu Guo-Yun1,Sozhamannan Shanmuga1112,Bradburne Christopher3,Palacios Gustavo15,

Affiliation:

1. Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA

2. Bioinformatics and Analytics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA

3. National Security Systems Biology Center, Asymmetric Operations Sector, Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA

4. U.S. Food and Drug Administration, Silver Spring, Maryland, USA

5. Filovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group, , University of Maryland at Baltimore, Baltimore, Maryland, USA

6. Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, Maryland, USA

7. Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA

8. FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA

9. Broad Institute, Cambridge, Massachusetts, USA

10. Virology, J. Craig Venter Institute, Rockville, Maryland, USA

11. The Threat Characterization Consortium, Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA

12. GoldBelt Raven, LLC, Frederick, Maryland, USA

Abstract

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 trade-offs 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.

Publisher

American Society for Microbiology

Subject

Virology,Microbiology

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