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???
I used finishing scripts for my work on sequencing of mitochondrial genome. Hope this will be useful for you as well. http://www.cbcb.umd.edu/finishing/
I used SSPACE-STANDARD to generate scaffold of my Salmonella typhi draft assembly. The only 'N' I found was on one contig as shown TAGAGAACCCTTCAATTGTTACGACAGGTCCAAATACTTCTTCTTGTACAATNCTCATAG
Is it still necessary for me to do gap filling?
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