Question: Preparing A Scaffolded Genome For Genbank Submission
5
gravatar for Rvosa
6.0 years ago by
Rvosa570
Leiden, the Netherlands
Rvosa570 wrote:

Hi,

I am preparing a vertebrate genome for submission to GenBank (WGS). The genome is organized in scaffolds (in one big FASTA file) for which we have genes predicted by maker (GFF3 file). In communicating with the NCBI staff it emerged that their WGS submission requirements have recently shifted - you no longer need to split scaffolds into contigs - but the process to go from what we have now to successful tbl2asn validation still seems too hairy to attempt to reinvent the wheel. So here is my question: is anyone aware of a tool(kit)/script that creates valid feature tables from a scaffolded genome?

Thanks,

Rutger

gff3 fasta genbank scaffolding • 2.2k views
ADD COMMENTlink modified 21 months ago by eennadi0 • written 6.0 years ago by Rvosa570
3
gravatar for brian@codenhance.com
5.2 years ago by
United States
brian@codenhance.com70 wrote:

Hi Rutger,

Way late to the party and still in beta, but if you're still looking to submit your genome you might try our software:

http://genomeannotation.github.io/GAG/

Let me know if you have any problems.

Aloha,

Brian

ADD COMMENTlink modified 4.8 years ago by Daniel Standage3.9k • written 5.2 years ago by brian@codenhance.com70
0
gravatar for eennadi
21 months ago by
eennadi0
eennadi0 wrote:

I have been trying to use GAG to prepare my genome for submission.

I generated the Gff file using maker but when I run it on GAG it tells me no parent

How do I solve this?

ADD COMMENTlink written 21 months ago by eennadi0
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