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