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
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.