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

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

1. Jason T. Ladner^a, 
2. Brett Beitzel^a, 
3. Patrick S. G. Chain^b,
4. Matthew G. Davenport^c, 
5. Eric Donaldson^d,^e, 
6. Matthew Frieman^f,
7. Jeffrey Kugelman^a, 
8. Jens H. Kuhn^e,^g, 
9. Jules O’Rear^d,^e, 
10. Pardis C. Sabeti^h,i,
11. David E. Wentworth^j, 
12. Michael R. Wiley^a, 
13. Guo-Yun Yu^a, 
14. The Threat Characterization Consortium^k, 
15. Shanmuga Sozhamannan^k,l,
16. Christopher Bradburne^c, 
17. Gustavo Palacios^a,^e

+Author Affiliations

1. aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
2. bBioinformatics and Analytics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
3. cNational Security Systems Biology Center, Asymmetric Operations Sector, Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA
4. dU.S. Food and Drug Administration, Silver Spring, Maryland, USA
5. eFilovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group
6. fDepartment of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, Maryland, USA
7. gIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
8. hFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
9. iBroad Institute, Cambridge, Massachusetts, USA
10. jVirology, J. Craig Venter Institute, Rockville, Maryland, USA
11. kThe Threat Characterization Consortium, Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA
12. lGoldBelt Raven, LLC, Frederick, Maryland, USA

1. Address correspondence to Jason T. Ladner, jason.t.ladner.ctr@mail.mil, or Gustavo Palacios, gustavo.f.palacios.ctr@mail.mil.

 

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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.