Related Experiment Video
Updated: Sep 29, 2025
08:31
Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
Published on: May 26, 2013
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The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction
Niema Moshiri1, Kathleen M Fisch2,3, Amanda Birmingham2
1Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA. niema@ucsd.edu.
Scientific Reports
|March 25, 2022
Summary
ViReflow is a user-friendly pipeline for rapid viral sequence analysis on the cloud. It enables quick reconstruction of viral consensus sequences for public health surveillance, even for large datasets.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- The COVID-19 pandemic highlighted the need for rapid SARS-CoV-2 strain surveillance.
- Massive sequencing and data sharing provided crucial public health information.
- Cloud computing offers high-performance computing but requires system administration expertise.
Purpose of the Study:
- To develop a user-friendly viral consensus sequence reconstruction pipeline.
- To leverage Amazon Web Services (AWS) cloud resources and the Reflow system for rapid viral data analysis.
- To create a tool applicable to any viral pathogen for molecular epidemiology.
Main Methods:
- Developed ViReflow, a pipeline integrating AWS cloud compute and the Reflow system.
- Designed for user-friendliness, flexibility, and scalability in viral sequence analysis.
- Automated processes including trimming, mapping, variant calling, and consensus sequencing.
Main Results:
- ViReflow enables rapid analysis of viral sequence datasets.
- Processes 1000 SARS-CoV-2 samples (1000X depth) in under 10 minutes with sufficient compute.
- Requires no user intervention for analysis completion.
Conclusions:
- ViReflow simplifies and accelerates viral molecular epidemiology.
- Its scalability and ease of use make it ideal for public health surveillance.
- The pipeline is a valuable tool for analyzing diverse viral pathogen sequence data.
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