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:
ACTAGGGAGGA -----GGGGGA
gets trimmed at:
ACTAGGGA|GGA -----GGG|GGA
when I want it to trim like:
ACTAG|GGAGGA -----|GGGGGA
I have tried --maxmatch and --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.
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