Question: How to force NUCmer to use exact match instead of unique match?
gravatar for nchuang
4.7 years ago by
United States
nchuang250 wrote:

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 --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.

nucmer alignment mummer • 1.3k views
ADD COMMENTlink written 4.7 years ago by nchuang250
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1003 users visited in the last hour