Yesterday I asked about same question and I got answer like below
"If 2 sequences originate next to one another in the genome, you can PCR using primers that face toward the junction to amplify the missing sequence. When you sequence that via Sanger sequencing, if the fragment overlaps both contigs, they are adjacent in the real genome." by jrj.healey
but I still didn't understand 100%.
I need an example about it.
1.Let's say there is a DNA sequence like,
5' ACCTAGCTGG 3'
2.And After NGS and genome assembly I got two scaffolds like,
scaffold1 : ACCTA scaffold2 : GCTGG
Can anyone who can explain with that?