Public Health Viral Genomics (PHVG): Overview

The Theiagen Public Health Viral Genomics repository hosts a collection of WDL workflows for characterization, epidemiology and sharing of the viral pathogen genomes. Currently, these focus on SARS-CoV-2, but workflows for other viral pathogens are anticipated to be available soon.

Getting Started

These workflows can be run at the command-line with Cromwell or miniWDL, but we strongly recommend use through Terra, a bioinformatics web application developed by the Broad Institute of MIT and Harvard in collaboration with Microsoft and Verily Life Sciences.

Running via a command-line interface

• Install miniWDL or Cromwell

• Install docker

• Clone Theiagen’s Public Health Viral Genomics git repository

• Run using miniWDL

Running via Terra

• Get started up with a Terra workspace

• Import the workflow into the Terra platform

A series of introductory training videos provide conceptual overviews the methodologies and tutorials on how to use our WDL workflows. For questions or general support regarding the WDL workflows in this repository, please contact support@theiagen.com