I am sorry for a very basic question. I sequenced a fungal genome with MiSeq (2*300) and I now finished a draft genome assembly with SPAdes (scaffold.fa). From the name, I understand it is assembled to scaffold level but it is very similar to another SPAdes output (contig.fa) although it has better stats. I am going to submit the genome to EMBL, and I can't make up my mind if it is OK to submit it as contig instead of scaffold? The genome is solely built on one paired-end library without mate-paired one.
Thanks in advance for advices.