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How to force NUCmer to use exact match instead of unique match?
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2.1 years ago
nchuang • 200
United States

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.