text: user1684: 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?
  
  user57: 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).
  
original_text: 1684: <p>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?</p>
  
  <p>Things I've tried so far:</p>
  
  <ol>
  <li><p>IMAGE from PAGIT. It asks for ace file which I guess is obtained from Newbler. So, I am not able to use this.</p></li>
  <li><p>gapfill_py script from broad: There are some gaps still missing.</p></li>
  </ol>
  
  <p>I came to know that Consed is good. But, I have windows which is not compatible for Consed. </p>
  
  <p>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?</p>
   57: <p>Assuming that gap filling is a domain-independent and works the same for viruses as for bacteria or eukarytes.</p>
  
  <p>There are two real options I am aware of: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0663-4" rel="nofollow noreferrer">Sealer</a> a successor of GapFiller from <a href="http://www.bcgsc.ca/platform/bioinfo/software/abyss" rel="nofollow noreferrer">ABySS</a> package and GapCloser from <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626529/" rel="nofollow noreferrer">SOAPdenovo2</a> 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).</p>
  