You were very helpful with my last assembly-related question, so perhaps you can help me again. I am trying to map an assembly I performed to an existing annotated genome. I assembled a wild sunflower sample and want to map it to an elite cultivar that has already been mapped and annotated. Are there any tools you recommend?
I am hoping to be able to submit the entire wild assembly file at once with the annotated elite cultivar assembly. Does such software exist? I was recommended BLAT, but that does not allow for enough sequence to be submitted.
Any and all help is appreciated :)