Overview

Genomic Epidemiology is an important approach in the effort to mitigate disease transmission. An often-critical step is generating phylogenetic trees to explore the genetic relationship between viruses on a local, national or global scale. The TheiaCoV Epidemiology Series facilitates this for SARS-CoV-2 by generating files for the visualization of phylogenetic trees with accompanying metadata.

The TheiaCoV Epidemiology Series contains two WDL workflows: TheiaCoV_Augur_Prep and TheiaCoV_Augur_Run. These must be run sequentially to first prepare each individual sample for running Augur, and second to run Augur itself on the set of samples, generating the phylogenetic tree files with accompanying metadata. The outputs from these workflows can be vizualised in Auspice and UShER.

<aside> ℹ️ Helpful resources for epidemiological interpretation

introduction to NextStrain (which includes Auspice)
guide to NextStrain interactive trees
an introduction to UShER
a video about how to read trees if this is new to you
documentation on how to identify SARS-CoV-2 recombinants </aside>

Overview

TheiaCoV_Augur_Prep

TheiaCoV_Augur_Run

Augur workflows reference

UShER references