Examples of Augur in the wild
Pathogen (link to Nextstrain)
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.