Preparing A Scaffolded Genome For Genbank Submission
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Entering edit mode
8.5 years ago
Rvosa ▴ 580

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

genbank gff3 fasta scaffolding • 2.8k views
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Entering edit mode
7.7 years ago

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

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Entering edit mode
4.3 years ago
eennadi • 0

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?

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