We are using DIAMOND 2.0.14 in our humann pipeline and we are wondering if it’s a good idea since humann seems to have been configured for the 0.9 version. Has it been tested? Can we pass some of the new options ?
We have not tested DIAMOND 2.0 within HUMAnN yet. I suspect it will work fine and provide some nice improvements. 
If you’d like to experiment, you could potentially try running it in the context of the HUMAnN 3 tutorial to see if it produces similar outputs:
That said, I’m not sure if DIAMOND 2.0 can work with the DIAMOND 0.9.36-formatted databases we bundle with HUMAnN 3 (the database format has changed a few times during development).
In HUMAnN 3 you can pass additional options to the DIAMOND binary via the --diamond-options flag (this should work across DIAMOND versions).
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