I have two sets of reads that were obtained from RNA bulks of resistant and susceptible wheat recombinant inbred lines. I am looking for polymorphism between the bulks. Based on previous results, I suspect that the polymorphism associated with the resistance is a large insert of 1-5kb (up to the whole gene). I also suspect that this insert is not present in the reference genome. I am looking for a software that can detect large structural variations using de-novo assembly.
Can you please recommend which software to use? Thank you