MUMmer aligments: How to visualize better the plots?

Question

[caro-ca]

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!

[Asaf]

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

Answer 1

[joneill4x]

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