Hi all!
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 :)
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peter_stokes •
There are several options, I will cite just two:
You can use LastZ, as Ensembl does.
You can use minimap2 - a tool I suspect will take over gradually and eventually become the go-to software for this kind of task.
edit: having read genomax comment, I understand now you want to find a web-based server to perform the alignment. Maybe there is a Galaxy server with lastz or minimap2 available, but I am not aware of one.
Hi there! Thanks for your response!
Does not have to be web based, I am happy using a command line/server based program as well.
+1 for minimap2, see also the cookbook: Full-Genome Alignment.
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You will have to do this computation on a local resource.
blat indeed is one option. You can use lastz (which was made to align chromosome size sequences) or even regular blast (megablast).