title: Standards for sequencing viral genomes in the era of high-throughput sequencing.
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.
authors.affiliation: Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA jason.t.ladner.ctr@mail.mil gustavo.f.palacios.ctr@mail.mil.
authors.forename: Jason T
authors.initials: JT
authors.lastname: Ladner
authors.affiliation: Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
authors.forename: Brett
authors.initials: B
authors.lastname: Beitzel
authors.affiliation: Bioinformatics and Analytics Team, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.affiliation: National Security Systems Biology Center, Asymmetric Operations Sector, Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA.
authors.forename: Matthew G
authors.initials: MG
authors.lastname: Davenport
authors.affiliation: U.S. Food and Drug Administration, Silver Spring, Maryland, USA Filovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group.
authors.forename: Eric F
authors.initials: EF
authors.lastname: Donaldson
authors.affiliation: Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, Maryland, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Frieman
authors.affiliation: Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Kugelman
authors.affiliation: Filovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA.
authors.forename: Jens H
authors.initials: JH
authors.lastname: Kuhn
authors.affiliation: U.S. Food and Drug Administration, Silver Spring, Maryland, USA Filovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group.
authors.forename: Jules
authors.initials: J
authors.lastname: O'Rear
authors.forename: Pardis C
authors.initials: PC
authors.lastname: Sabeti
authors.affiliation: Virology, J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Wentworth
authors.affiliation: Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Wiley
authors.affiliation: Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA.
authors.forename: Guo-Yun
authors.initials: GY
authors.lastname: Yu
authors.forename: Shanmuga
authors.initials: S
authors.lastname: Sozhamannan
authors.affiliation: National Security Systems Biology Center, Asymmetric Operations Sector, Johns Hopkins University, Applied Physics Laboratory, Laurel, Maryland, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Bradburne
authors.affiliation: Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA Filovirus Animal Nonclinical Group (FANG) Well Characterized Challenge Material Working Group jason.t.ladner.ctr@mail.mil gustavo.f.palacios.ctr@mail.mil.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Palacios
mesh_terms: D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods / Q000592:standards*; D014780:Viruses / Q000235:genetics*