I have assembled poxvirus genome using Ray. The assembly is good. Out of several thousand contigs I got, I was able to get one scaffold using Contiguator tool, which is about 90% of my genome. I have well annotated reference sequence. If there any good tool for filling gaps and checking assembly quality?
Things I've tried so far:
IMAGE from PAGIT. It asks for ace file which I guess is obtained from Newbler. So, I am not able to use this.
gapfill_py script from broad: There are some gaps still missing.
I came to know that Consed is good. But, I have windows which is not compatible for Consed.
I checked my BAM file with Tablet. There are reads that cover almost entire gene. Are there any good tools or manual ways to finish my assembly so that I can get the full genome?