Implement and evaluate a new long-read-specialized tandem repeat finder about long-read-pipelines HOT 1 OPEN

I looked into this, and it's not really clear to me that NCRF is meant for use in the way we're expecting. It takes as input a fasta file, and it's not clear to me how to run this as a discovery tool. In fact, from the documentation:

Note that this is not intended to be a turnkey solution but more of an exploratory platform for the user. It will likely require parameter tweaking and experimentation on the part of the user, as well as some user-written programs to post-process the output.

I don't think this is what we want. I think we're going to need to look more expansively at specialized repeat expansion/contraction callers for long read data.

from long-read-pipelines.