Question: Bulk Rast To Ncbi/Ebi/Genbank
gravatar for c.v.oflynn
7.4 years ago by
United Kingdom
c.v.oflynn100 wrote:

Hi Everyone,

I cant find anyone else with this problem anywhere so maybe i've missed something..

I have ~200 bacterial genomes that i have assembled, they come from a range of taxa.

What i would like to do is upload them to GenBank, so that they are ready for when i publish.

My problem is that i cant find any obvious way to do this in bulk without spending a lot of time filling in web forms. I know ebi has a bulk upload, via webin, but i think this is meant for closely related species(?), mine aren't.

My second issue is that i annotated them using RAST and i would like to use this information for the published genomes, i know you can make this public but that doesn't feel right and is not really what i'm after.

Is there an automated way of doing this? ideally, ideally, something like curl where can just upload the contigs(.fa) the annotation (gtf/genbank) and metadata (.txt), and it just gets sorted?

Thanks Guys,


ADD COMMENTlink modified 7.4 years ago by Michael Dondrup47k • written 7.4 years ago by c.v.oflynn100

Did you see this?

ADD REPLYlink written 7.4 years ago by Michael Dondrup47k
gravatar for Michael Dondrup
7.4 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Maybe the Sequin tool is for you? When you look at requirements for a good annotation they are quite strict, e.g. with respect to naming. But you can also have NCBI run an automatic annotation after the upload, that might be less work for you overall.

ADD COMMENTlink written 7.4 years ago by Michael Dondrup47k
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