Journal
SCIENTIFIC REPORTS
Volume 12, Issue 1, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41598-022-09035-w
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Funding
- US National Science Foundation [2028040, 2038509, 1659104]
- Centers of Disease Control and Prevention [75D30120C09795]
- National Institutes of Health [UL1TR001442]
- UC San Diego Office of the Chancellor
- National Institutes of Health SIG grant [S10 OD026929]
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [1659104] Funding Source: National Science Foundation
- Division Of Environmental Biology
- Direct For Biological Sciences [2028040] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [2038509] Funding Source: National Science Foundation
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During the COVID-19 pandemic, the development of a user-friendly tool called ViReflow, utilizing Amazon Web Services and Reflow system, has enabled rapid analysis of viral sequence data, contributing to the efficient monitoring of SARS-CoV-2 strains worldwide.
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.
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