[Feature Request] Many-vs-Many upper triangle of pairwise genome ANI calculation

[jolespin]

A new tool called skani has a very convenient option that avoids a lot of duplicate computation:
https://github.com/bluenote-1577/skani/wiki/skani-basic-usage-guide#skani-triangle---all-to-all-ani-computation

Here's a screenshot:

Would it be possible for FastANI to use this functionality as well to only calculate the upper triangle?

[cjain7]

The current implementation of FastANI indexes all genomes in the reference list at the preprocessing stage. The index is not changed afterwards when each query genome is processed. As a result, doing n^2 computations is more convenient for us.

We can try periodically recomputing the index with fewer genomes. I am not sure how much time we will gain by this.

[jolespin]

Would it be possible to provide a single list, index all of the genomes, and then query each non redundant pair?

I was thinking of implementing a wrapper to do the pairs myself and call FastANI around it but then realized the index would be created for each process.

I'm currently having memory issues with FastANI and I think the n^2 might be the culprit.

[jolespin]

Also, if you provide a list of 1k genomes for --rl and the same list for --ql, does it calculate the index of each genome twice?