We want Nextstrain to be a community-driven platform, to share datasets with collaborators and the world.
While you can install
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.
Store your final output from augur, i.e. the JSONs which auspice uses, in a directory called “auspice” — see here for an example
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.
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.