I have two pacbio assemblies for the same plant species, and I need to determine if there are regions represented in one assembly that are missing from the other. I have tried using progressiveMauve, and while I suspect that the information I'm looking for is somewhere in the output I'm having a hard time finding it.
Does anyone have a solution to this problem?
as an update, here are stats on one of the assemblies -- the other is similar to this.
number of contigs: 18355
mean contig size: 27903.8
median contig size: 15781
total size: 512174223
Pretty much every contig is big enough to include repetitive elements of some sort, so blastn output is not of much value.