Maybe a simple question but for which I am unable to find documentation on NCBI, by their support, or here at BioStar thus far.
Use case: I currently have 30+ draft genomes/large-plasmids (scaffolded contigs) and want to submit these to NCBI to get accession numbers for publication.
Approach: The new guidelines make it obligatory to register a bioproject first, then make for each sample/genome a Biosample entry and subsequently link a WGS submission to that. Clear. I created a bioproject, I batch uploaded the biosample collection using their template. No problem. Bioproject and biosamples succesfully registered.
Problem: Using their WGS submission pipeline online I have to supply fasta files of all contigs (not a problem) and an AGP-v2 file describing the scaffolding (not a problem I generated those). BUT, I seem to have to manually upload each of these files for every single biosample one-by-one. Not that bad, but I also need to provide 6 pages full of selection boxes or extensive author/publication information for EACH biosample one-at-a-time. Makes me sad and is error-prone.
Question: How can I batch upload these samples and get them linked to my biosamples properly? All WGS linked data are more or less the same (publication, type, authors, .....). In the future we plan to do 100+ of these...