Merge Scaffolds From Different Individuals?

Question

[Gabriel R.]

I have scaffolds from two different individuals of the same species (eukaryotic). I seek to merge scaffolds that overlap each other by first finding significant overlaps between scaffolds and calling a consensus on the overlapped regions to obtain longer and (hopefully) more correct scaffolds. I don't care about losing phasing information. Is there a tool to do this ?

Answer 1

[Andrzej Zielezinski]

Use CAP3, a very popular DNA sequence assembly program that generates a consensus sequences.

The CAP3 program is available at http://seq.cs.iastate.edu/cap3.html

Server for CAP3 is available at http://deepc2.psi.iastate.edu/aat/cap/cap.html