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Guest Editorial

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 Donaldson, Matthew Frieman, Jeffrey Kugelman, Jens H. Kuhn, Jules O’Rear, Pardis C. Sabeti, David E. Wentworth, Michael R. Wiley, Guo-Yun Yu, The Threat Characterization Consortium, Shanmuga Sozhamannan, Christopher Bradburne, Gustavo Palacios
Jason T. Ladner
aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
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Brett Beitzel
aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
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Patrick S. G. Chain
bBioinformatics and Analytics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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Matthew G. Davenport
cNational Security Systems Biology Center, Asymmetric Operations Sector, Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA
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Eric Donaldson
dU.S. Food and Drug Administration, Silver Spring, Maryland, USA
eFilovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group, , University of Maryland at Baltimore, Baltimore, Maryland, USA
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Matthew Frieman
fDepartment of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, Maryland, USA
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Jeffrey Kugelman
aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
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Jens H. Kuhn
eFilovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group, , University of Maryland at Baltimore, Baltimore, Maryland, USA
gIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
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Jules O’Rear
dU.S. Food and Drug Administration, Silver Spring, Maryland, USA
eFilovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group, , University of Maryland at Baltimore, Baltimore, Maryland, USA
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Pardis C. Sabeti
hFAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
iBroad Institute, Cambridge, Massachusetts, USA
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David E. Wentworth
jVirology, J. Craig Venter Institute, Rockville, Maryland, USA
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Michael R. Wiley
aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
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Guo-Yun Yu
aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
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kThe Threat Characterization Consortium, Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA
Shanmuga Sozhamannan
kThe Threat Characterization Consortium, Defense Threat Reduction Agency, Fort Belvoir, Virginia, USA
lGoldBelt Raven, LLC, Frederick, Maryland, USA
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Christopher Bradburne
cNational Security Systems Biology Center, Asymmetric Operations Sector, Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA
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Gustavo Palacios
aCenter for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
eFilovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group, , University of Maryland at Baltimore, Baltimore, Maryland, USA
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DOI: 10.1128/mBio.01360-14
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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.

The views expressed in this article do not necessarily reflect the views of the journal or of ASM.

  • Copyright © 2014 Ladner et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

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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 Donaldson, Matthew Frieman, Jeffrey Kugelman, Jens H. Kuhn, Jules O’Rear, Pardis C. Sabeti, David E. Wentworth, Michael R. Wiley, Guo-Yun Yu, The Threat Characterization Consortium, Shanmuga Sozhamannan, Christopher Bradburne, Gustavo Palacios
mBio Jun 2014, 5 (3) e01360-14; DOI: 10.1128/mBio.01360-14

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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 Donaldson, Matthew Frieman, Jeffrey Kugelman, Jens H. Kuhn, Jules O’Rear, Pardis C. Sabeti, David E. Wentworth, Michael R. Wiley, Guo-Yun Yu, The Threat Characterization Consortium, Shanmuga Sozhamannan, Christopher Bradburne, Gustavo Palacios
mBio Jun 2014, 5 (3) e01360-14; DOI: 10.1128/mBio.01360-14
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  • Article
    • ABSTRACT
    • EDITORIAL
    • PROPOSED CATEGORIES FOR WHOLE-GENOME SEQUENCING OF VIRUSES
    • ADDITIONAL HIGH-THROUGHPUT SEQUENCE-BASED GENOME CHARACTERIZATIONS
    • RECOMMENDED STANDARDS FOR DOWNSTREAM APPLICATIONS
    • REPOSITORIES OF GENOMIC INFORMATION AND DATA CURATION
    • ACKNOWLEDGMENTS
    • REFERENCES
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