Viral genome finishing 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?
Assuming that gap filling is a domain-independent and works the same for viruses as for bacteria or eukarytes.

There are two real options I am aware of: Sealer a successor of GapFiller from ABySS package and GapCloser from SOAPdenovo2 package. According to Sealer paper it's better, but I am not sure if any indepented benchmarking have confirmed their conclusion. On my insect data GapCloser worked better than GapFiller (back then I have not tried to compare it to Sealer).