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, th...
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American Society for Microbiology
2014
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oai:doaj.org-article:4dd7e67cfafd4f7da255f86e67a2e10e2021-11-15T15:47:39ZStandards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing10.1128/mBio.01360-142150-7511https://doaj.org/article/4dd7e67cfafd4f7da255f86e67a2e10e2014-07-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01360-14https://doaj.org/toc/2150-7511ABSTRACT 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.Jason T. LadnerBrett BeitzelPatrick S. G. ChainMatthew G. DavenportEric DonaldsonMatthew FriemanJeffrey KugelmanJens H. KuhnJules O’RearPardis C. SabetiDavid E. WentworthMichael R. WileyGuo-Yun YuShanmuga SozhamannanChristopher BradburneGustavo PalaciosAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 3 (2014) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Microbiology QR1-502 |
| spellingShingle |
Microbiology QR1-502 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 Shanmuga Sozhamannan Christopher Bradburne Gustavo Palacios Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing |
| description |
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. |
| format |
article |
| author |
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 Shanmuga Sozhamannan Christopher Bradburne Gustavo Palacios |
| author_facet |
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 Shanmuga Sozhamannan Christopher Bradburne Gustavo Palacios |
| author_sort |
Jason T. Ladner |
| title |
Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing |
| title_short |
Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing |
| title_full |
Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing |
| title_fullStr |
Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing |
| title_full_unstemmed |
Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing |
| title_sort |
standards for sequencing viral genomes in the era of high-throughput sequencing |
| publisher |
American Society for Microbiology |
| publishDate |
2014 |
| url |
https://doaj.org/article/4dd7e67cfafd4f7da255f86e67a2e10e |
| work_keys_str_mv |
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