how to show geographical relationship of contigs from the two assemblies

Question

[Mehmet]

Dear All,

I want to compare some contigs from two different assemblies of the same animal species. For instance, I want to compare a big contig from assembly A. The big contig will contain small contigs from assembly B. I also want to show haplotype collapse between the assembly A and assembly B.

Which tools/programs and flowchart do you suggest?

Thank you

Answer 1

[h.mon]

Mauve is one of the easiest to use and has a graphical interface with some (on my opinion) nice graphic presentation of the results.