Diamond not used for the transport-find command about gapseq HOT 2 CLOSED

Hi Jan,

diamond is also not used in find:

Note the hash before the diamond call.

We once considered diamond as an alternative, ran some tests, and noticed that diamond wouldn't improve runtime in how gapseq performs the searches, at least without being too invasive in the rest of the code.

Concerning the snakemake pipeline: Have a look at https://github.com/Waschina/gapsnake

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Cool thanks - than I misunderstood Johannes and just failed to notice the usage of blastp in the find command.

I just looked through the code and I can see now why that is. For diamond to improve speed, you would need to concatenate the different query sequence files into one query - that would speed up things a lot. But it would also require a lot of reshaping the original code.

Maybe, we can organize a small hackathon on the topic at some point. Than I would gladly help out implementing it. But I will close the issue for now.

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