<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>If you use paired reads you can take a look to: <a href='http://www.biomedcentral.com/1471-2105/13/S14/S8'>GapFiller</a> </p>

<p>I haven't test it myself, though.</p>
