How to force NUCmer to use exact match instead of unique match?
I am trying to snip off the flanks of my query sequence when aligning to a reference sequence using Nucmer. I noticed that the alignment:
gets trimmed at:
when I want it to trim like:
I have tried
--nosimplifiy but it doesn't seem to change the coordinates that it outputs in the
.coords file. It has this similar issue with the 3' flank as well.