<p>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??? </p>

<p>There are a few in silico tools that can fill in the gaps within scaffolds;</p>

<p>GapFiller (developed by myself, I'm also the developer of SSPACE):
<a href='http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/'>http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/gapfiller/</a>
<a href='http://genomebiology.com/2012/13/6/R56'>http://genomebiology.com/2012/13/6/R56</a></p>

<p>IMAGE2:
<a href='http://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page'>http://sourceforge.net/apps/mediawiki/image2/index.php?title=Main_Page</a></p>

<p>GapCloser (part of SOAP):
<a href='http://sourceforge.net/projects/soapdenovo2/files/GapCloser/'>http://sourceforge.net/projects/soapdenovo2/files/GapCloser/</a></p>

<p>Regards,
Boetsie</p>
