I have been searching this subject and trying to find a technique that fits my needs and so far I have been having no success.
I am looking to test try and find crossover events in my HiSeq datasets. I have 9 strains of the same non-model clonal species that are very similar to each other in that sense that a lot of genomic variation due to ploidy is shared. I am now interested if despite clonal propagation, there is still recombination occurring.
All I have is 9 HiSeq 100bp x 2 PE reads with a fragment size of ~300bp for my 9 strains.