Hi every one i am doing some plamid genome assembly with spades. After assembly i used SSPACE for scaffolding. But there are some gap each of the draft genome. I can fill the gap by PCR. But i want to reduce the number of gap insilico?? Can anyone suggest how to reduce the gap ?? If i do mapping the reads with contigs will it be give any promising result???
There are a few in silico tools that can fill in the gaps within scaffolds;
GapFiller (developed by myself, I'm also the developer of SSPACE): http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/ http://genomebiology.com/2012/13/6/R56
GapCloser (part of SOAP): http://sourceforge.net/projects/soapdenovo2/files/GapCloser/
Your genome is circular, correct?
Your current assembly resulted in the entire genome as a scaffold with gaps (NNNs), but otherwise, your scaffold is circular, correct?
You can try iterative read mapping. You can do that either with CONSED (free) or Geneious (14 day free trial). When you map iteratively, each time an iteration is complete, the idea is that your contigs will be extended slightly. At one point, they should overlap. The bigger the read lengths, the faster you will be done.