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Compatibility between Augur & Auspice versions

From mid-2019, we're changing the format of the output file produced by augur export to allow more flexibility going forward. This lines up with the version 2 release of auspice (release notes), which opens up exciting new possibilities.

We also recognise that we may need to adjust things again in the future. By setting up versions now, we'll be able to continue to expand augur and auspice while minimizing disruption to users.

You can get more information on how to move to using export v2 in augur v6.0 in our handy guide.

Why does compatibility matter?

To get great visualisations, the final step of the augur pipeline, augur export produces output as one or more JSON files*. The JSON(s) are then read by auspice to produce trees, graphs, and maps.

*This compatibility only refers to the JSON file(s) produced by augur export, not those produced by other augur steps.

Different augur versions will produce different JSON output formats, which in turn will work with different auspice versions. We aim to support backwards compatibility as much as possible, and of course, if you're you're using the latest augur, JSON, and auspice versions, everything will work smoothly!

Whenever possible, we recommend updating your run to work with the latest augur and outputing the most recent JSON format to view with the latest auspice - it future-proofs your work and ensures you'll benefit from all the latest features and improvements.

But, we know that for a variety of reasons, you can't always do this straight away. To help keep your research flowing, here are some tables of how different versions of augur, export JSONs, and auspice are compatible.

Compatibility Tables

Augur

Augur Version Produces JSON Works with Auspice
v5 v1 (via export) v1 & v2
v6 v1 (via export v1)
v2 (via export v2)
v1 & v2

JSON versions

JSON Version Produced by Augur Version Works with Auspice
v1 (meta + tree) v5 (via export)
v6 (via export v1)
v1 & v2
v2 v6 (via export v2) v2

Auspice

Auspice Version Takes JSON
v1 v1
v2 v1 or v2