Community Sharing of Results Via GitHub

We want Nextstrain to be a community-driven platform, to share datasets with collaborators and the world. While you can install augur and auspice locally to analyse and interact with datasets, we wanted a way to share these with the world — without having to lose control of your data.

Our solution to this is to allow anyone to store the results of their analyses on GitHub but still analyse them through nextstrain.org. This gives you complete control, ownership, and discretion over your data.

How Does This Actually Work?

  • Run your analysis locally (see the bioinformatics introduction)
  • Create a github repository for your analysis. For instance, Alli Black has created a “zika-colombia” in the “blab” group/organisation/username — github.com/blab/zika-colombia

    • This is your own github repository — you don’t even need to tell us about it if you don’t want to!
  • Make sure the JSONs you’ve produced start with the same name as the repository. In this case they’d need to be zika-colombia_meta.json and zika-colombia_tree.json
  • Store your final output from augur, i.e. the JSONs which auspice uses, in a directory called “auspice” — see here for an example

    • While you don’t need to, it’d be great if you also stored your analysis pipeline (e.g. Snakefile) on GitHub too! This doesn’t need to give away any data, just the recipe for the analysis.
  • Push things to github.
  • Access your data via “nextstrain.org/community” + “github organisation name” + “github repo name”. For this example, it’s at nextstrain.org/community/blab/zika-colombia.

    • Share your results with the world 🎉🎉

Some Examples

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 nextstrain.org 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, Allison Black, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Garten, Dylan George, Ian Goodfellow, Nathan Grubaugh, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Louise Moncla, 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.

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© 2015-2019 Trevor Bedford and Richard Neher