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Related Experiment Video

Updated: Jun 27, 2026

Whole Genome Sequencing for Rapid Characterization of Rabies Virus Using Nanopore Technology
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From Bench to Insight: Rapid Pathogen Genomic Surveillance Workflow for SARS-CoV-2 and Emerging Pathogens.

Chelsea Zimmer1, Selena McVay1, Keely Starke1

  • 1Office of Research, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43201, USA.

Genes
|June 26, 2026
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Summary

A new workflow pipeline simplifies SARS-CoV-2 genomic analysis for surveillance labs. This system efficiently identifies mutations and variants, integrating data into REDCap for streamlined reporting and enhanced public health response.

Keywords:
S5 ion torrent suiteWDL workflowcladelineage

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Area of Science:

  • Genomics
  • Bioinformatics
  • Epidemiology

Background:

  • Clinical surveillance of viral infectious diseases like SARS-CoV-2 is crucial for pandemic prevention.
  • Advancements in whole genome sequencing generate vast amounts of viral data for evolutionary studies.
  • Surveillance labs require efficient bioinformatics pipelines to manage high sample volumes and report mutations.

Purpose of the Study:

  • To develop a streamlined, user-friendly pipeline for SARS-CoV-2 mutational analysis.
  • To enable surveillance labs with minimal bioinformatics expertise to handle large-scale genomic data.
  • To integrate variant data into a centralized database for efficient reporting.

Main Methods:

  • Developed an open-source SARS-CoV-2 mutational analysis pipeline using Workflow Description Language (WDL).
  • The pipeline processes sequencing data, performs clade and variant assignments, and integrates patient metadata.
  • Results are stored in a REDCap database, with an interactive dashboard for real-time monitoring and reporting.

Main Results:

  • The WDL pipeline provides a human-readable and adaptable workflow for genomic data analysis.
  • REDCap serves as a robust data backbone for tracking and storing analysis results.
  • An interactive dashboard enhances data visualization and facilitates consolidated variant report generation.

Conclusions:

  • The developed approach streamlines the management of complex genomic data for infectious disease surveillance.
  • The pipeline is easily adaptable, empowering molecular labs to enhance their variant reporting capabilities.
  • This system supports efficient identification and reporting of viral mutations, aiding public health interventions.