I have bacterial genome sequenced by Illumina technology, the genome was de novo assembled by SPAdes assembler, I got 38 contigs. The contigs were reordered by Mauve using close reference genome. my question, is it correct to remove the headers between the contigs to produce only one scaffolds and do the annotation by PGAP tool? if I submit to NCBI in this case it will be accepted?
BTW, I tried to use gap filling tools, but that has no any effect.
I appreciate any help or advice in advance.