Examples of Augur in the wild

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.

Nextstrain tutorials

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.

Nextstrain pathogens

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.

Pathogen

GitHub repository

Seasonal influenza

nextstrain/seasonal-flu

West Nile Virus

nextstrain/WNV

Lassa

nextstrain/lassa

Mumps

nextstrain/mumps

Zika

nextstrain/zika

Ebola

nextstrain/ebola

Dengue

nextstrain/dengue

Avian influenza

nextstrain/avian-flu

Measles

nextstrain/measles

Enterovirus D68

neherlab/enterovirus_nextstrain

Tuberculosis

nextstrain/tb

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 community

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