I want to ask if there is anything out there that might help me do this before I start to spend too much time trying to hack it together. I have a set of very long >10kb nanopore reads that theoretically contain the same 4kb region within over and over in the same orientation. Is there an easy way to align all of the individual repeats of this region to said region?
I was thinking of iterating through all reads, do a local alignment of the region and store the aligned part in a sub read set, hence computationally fragmenting all of the reads. But maybe there is a more elegant way of doing this?
Thanks for all the advice Conradin