The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
24 03 2022
24 03 2022
Historique:
received:
02
11
2021
accepted:
15
03
2022
entrez:
25
3
2022
pubmed:
26
3
2022
medline:
5
4
2022
Statut:
epublish
Résumé
Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, with great sequencing comes great computation, and while cloud computing platforms bring high-performance computing directly into the hands of all who seek it, optimal design and configuration of a cloud compute cluster requires significant system administration expertise. We developed ViReflow, a user-friendly viral consensus sequence reconstruction pipeline enabling rapid analysis of viral sequence datasets leveraging Amazon Web Services (AWS) cloud compute resources and the Reflow system. ViReflow was developed specifically in response to the COVID-19 pandemic, but it is general to any viral pathogen. Importantly, when utilized with sufficient compute resources, ViReflow can trim, map, call variants, and call consensus sequences from amplicon sequence data from 1000 SARS-CoV-2 samples at 1000X depth in < 10 min, with no user intervention. ViReflow's simplicity, flexibility, and scalability make it an ideal tool for viral molecular epidemiological efforts.
Identifiants
pubmed: 35332213
doi: 10.1038/s41598-022-09035-w
pii: 10.1038/s41598-022-09035-w
pmc: PMC8943356
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
5077Subventions
Organisme : CDC HHS
ID : 75D30120C09795
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001442
Pays : United States
Organisme : NIH HHS
ID : S10 OD026929
Pays : United States
Organisme : National Science Foundation
ID : 2038509
Organisme : National Science Foundation
ID : 2028040
Informations de copyright
© 2022. The Author(s).
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