Couple of months back, I sequenced (MiSeq) few BACs and assembled (Paired-end reads) using SOAPdenovo, but my assembly was fallen into many scaffolds. Now, I got reference genome and trying to pull out my interested region (about 3.2 Mb).
Here is my first approach:
I mapped paired-end reads to the reference genome and parsed out the scaffolds, those got mapped. Still, 3.2 Mb of my region is spreaded into 26 scaffolds. I believe, I can able to close these gaps with my Paired-end data. I also got genome of other three very related species to aid me in gap closing.
Now, my question is, what would be the best approach to close gaps?
Many thanks in advance