Question: Mapping assembly to existing annotated genome
1
gravatar for peter_stokes
23 months ago by
peter_stokes10
peter_stokes10 wrote:

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 :)

assembly • 652 views
ADD COMMENTlink modified 23 months ago by h.mon29k • written 23 months ago by peter_stokes10
1

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).

ADD REPLYlink written 23 months ago by genomax80k
3
gravatar for h.mon
23 months ago by
h.mon29k
Brazil
h.mon29k wrote:

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.

ADD COMMENTlink modified 23 months ago • written 23 months ago by h.mon29k
1

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

ADD REPLYlink written 23 months ago by WouterDeCoster43k

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.

ADD REPLYlink written 23 months ago by peter_stokes10
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