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how to show geographical relationship of contigs from the two assemblies

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

assembly sequencing alignment gene
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updated by h.mon h.mon • written by Mehmet Mehmet

1 answer

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

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written by h.mon h.mon

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