Question: MUMmer aligments: How to visualize better the plots?
0
gravatar for caro-ca
5 months ago by
caro-ca0
caro-ca0 wrote:

Hi! I already aligned my assemblies from Nanopore long reads, but when I tried to look at the .png file from MUMmer is very difficult to visualize the contigs of the x and y axes. Do you have any recommendation on how to visualize the plots better? Thank you in advance!

mummerplots • 351 views
ADD COMMENTlink modified 4 months ago by joneill4x70 • written 5 months ago by caro-ca0
1

Can you show an example? If you're referring to the diagonals plot you might want to intersect it, for instance show one contig vs the other genome of several contigs, you will need to select lines from the out.delta file and change the fasta files

ADD REPLYlink written 4 months ago by Asaf7.2k
2
gravatar for joneill4x
4 months ago by
joneill4x70
Canada
joneill4x70 wrote:

Genome Ribbon

http://genomeribbon.com/

https://youtu.be/Ih4Wf2U10-4

D-GENIES usues minimap2 rather than MUMmer. I have found it extremely useful.

http://dgenies.toulouse.inra.fr/run

ADD COMMENTlink modified 4 months ago • written 4 months ago by joneill4x70
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