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.
There are three tutorials for getting started with Nextstrain that use Augur for all or part of the bioinformatics and analysis:
The Zika tutorial is a good starting point if you have FASTA files and some metadata about your sequences. The accompanying build repository is a simplified version of the full Zika build.
The Tuberculosis tutorial is a good starting point if you have VCF files and some metadata about your sequences. It uses the full Tuberculosis build repository.
The MERS / BEAST tutorial is a good starting point if you have a BEAST tree and want to use it with Augur and Auspice.
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.
There are also some community-produced analyses on Nextstrain which use Augur:
| Name | GitHub repository |
|---|---|
| Ebola epidemic in North Kivu, DRC | inrb-drc/ebola-nord-kivu |
| Wheat yellow rust | SaundersLab/PST |