<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><a href='http://soap.genomics.org.cn/soapdenovo.html'>GapCloser</a> from SOAPdenono works perfect for me. <br />
To use it, you will need paired-end or mate-pair reads. </p>
