Augur: Nextstrain's Bioinformatics Toolkit

Nextstrain’s bioinformatics toolkit is called Augur. It is a core part of the Nextstrain ecosystem used by all of our pathogen builds, and all source code is available on GitHub.

Augur provides ways to perform common bioinformatics tasks through a collection of commands which are designed to be composable into larger processing pipelines. This means the commands work well both independently and together, embracing the philosophy of composability.

We’ve used Augur to analyze a bunch of different pathogens — from viruses with tiny genomes like Zika, to bacterial genomes orders-of-magnitude bigger like tuberculosis. Check out the tutorials (via the sidebar to the left) to see which components we used in each one.

Since we built it to be composable, it’s easy to use other code or software to replace steps (or multiple steps!). Similarly, not all available commands are applicable — nor scientifically valid — for different pathogen analyses. We’ve used BEAST to replace multiple augur commands, but still visualize the results in auspice. It’s also common to have additional scripts which are called in-between different components; reading the different tutorials should give you a feel for how powerful these can be, and how versatile your builds can be!

Explore in more depth:

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to must be provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.


© 2015-2020 Trevor Bedford and Richard Neher