I have 5 strains mixed in culture and propagated and I am trying to measure recombination rates by sequencing total DNA extracted after certain periods of time.
One way would probably be to extract paired end reads that map to different strains (forward reads maps to strain A reverse read maps to strain B). In this case, the recombination (cross over) event happend in the unsequenced part between the paired reads.
I am interested in finding all cases where reads of the same pair mapped to different references. I am sure there are other wise of spotting recombination and I will look into it, but this is a good way to start.