Scaffolding of bacterial genome assemblies

Question

[Jelo]

Hi everyone,

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.

thank you

[andres.firrincieli]

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?

No, you can't remove the headers and produce only one scaffold. The Mauve analysis only guess the order of the contigs based on a close reference genome. You must perform a PCR to confirm the exact order

[Jelo]

I appreciate your reply

[samuel.a.odonnell]

Generally scaffolding works somewhat like that except 'N's are placed in between the contigs to signify that they have been scaffolded together after assembly. This is only done within chromosomes too.