Mapping assembly to existing annotated genome

Question

[peter_stokes]

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 :)

[GenoMax]

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).

Answer 1

[h.mon]

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.

[WouterDeCoster]

+1 for minimap2, see also the cookbook: Full-Genome Alignment.

[peter_stokes]

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.