I got multiple assemblies that were created by using different programs. These assemblies originated from genomes of different individuals from the same species, so they are expected to show high similarity.
I started by running the command
nucmer --minalign=100 -p <name> <query-sequence> <reference-sequence>, and then the command
mummerplot --png output.delta, which yielded a graph with scattered dots, instead of the expected diagonal line.
I wanted to ask if there's something in the commands that caused these results. Maybe the command needs certain parameters. I didn't know which ones to use.
I used samuel.a.odonell's advise and got an improved plot, yet I'm still having issues. The dots are rather scattered. I thought about using matches of 1000 bp or more, and I've been looking for a way to rearrange the contigs so that the plot will show a diagonal line. Also, I'm looking for a way to modify the axes tags, so that instead of having a smear of innumerable tags, there will be a numeric scale.
I've been looking for solutions for these issues for the last two days but couldn't find any. I'm sure they're there somewhere but I guess it's a needle in the haystack situation.
Here's one of the plots I got: mummerplot output