We really enjoy hearing about people using Augur. If you use Augur to do your work, we'd love to add it to this page! Let us know about it by opening an issue or submitting a PR.
All pathogens on Nextstrain currently use Augur to go from raw data to Auspice-ready results files by performing cleanup, subsampling, alignment, tree building, and ancestral state reconstruction.
Each pathogen has its own build repository on GitHub which uses Snakemake to define and run the pipeline of Augur commands.
You can download a copy of a build repository, inspect the Augur commands used, and try running it locally yourself. This can be useful to reproduce the analysis or tweak it for your own needs and data.
Nextstrain also provides access to analyses by independent groups stored and accessed via public GitHub repos, all of which currently use augur. For the most up-to-date listing of these please see the community section on the nextstrain front page.