What's the right way to submit a genome assembly to NCBI?

Question

[liorglic]

Hi everybody, I'd like to submit an eukaryotic assembly to NCBI. I've gone through the Genome submission guide, but am still not clear on what's exactly expected and would like some advice from someone who did this lately.
I have all three levels of the assembly: contigs, scaffolds and chromosomes. Each contig is part of a scaffold (some scaffolds consist of a single contig). Most scaffolds are mapped to a chromosome location, but there are also unplaced scaffolds (no chromosome assignment). Which of the following options is expected/recommended?

1. A single fasta file with chromosomes, scaffolds and contigs + an AGP file to indicate contigs and scaffold locations
2. Three fasta files - one for contigs, one for scaffolds and one for chromosomes + AGP file to indicate contigs and scaffold locations
3. Give up the AGP file - just upload fasta file/s (options 1 or 2)
4. Give up the contigs - only upload scaffolds and chromosomes + AGP
5. Something else...

Thanks a lot!

[GenoMax]

While you wait for answers I would suggest sending this question to NCBI help desk. So you get information from "horse's mouth", so to speak.

Answer 1

[liorglic]

I ended up contacting NCBI help desk (as suggested by @genomax). Here's the answer I got:

We recommend you to submit the gapped scaffold fasta file and answer the gap questions on the submission portal, along with the agp file that includes the chromosomes and the unplaced scaffolds. You can split the agp file into 2 files (one for chromosomes and the other for the unplaced scaffolds) if you want.

[Philipp Bayer]

As an aside, if you're with an Australian institution you can use EMBL-ABR's data chaperoning service, they will do this work for you : https://www.embl-abr.org.au/data-chaperoning/