Overview

Genomic Epidemiology is an important approach in the effort to understand and mitigate against disease transmission. An often-critical step in viral genomic epidemiology is the generation of phylogenetic trees to explore the genetic relationship between viruses on a local, regional, national or global scale. The Augur workflows, currently only targetted for viral pathogens, facilitate this process by generating files for the visualization of phylogenetic trees with accompanying metadata.

Two workflows are offered: Augur_Prep_PHB and Augur_PHB. These must be run sequentially, respectively, to first prepare each individual sample for running Augur, and secondly to run Augur itself on the set of samples, generating the phylogenetic tree files with accompanying metadata. The outputs from these workflows can be visualized 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>

Augur_Prep_PHB

Augur_PHB

References

✉️ [email protected] | X (formerly Twitter) | LinkedIn | 🌐 Website