Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-10T19:35:38.223Z
Answers.Text: Can you please tell what input files do Sealer and GapFiller take ?
Answers.UserDisplayName: LoveVirology
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-12T07:59:21.667Z
Answers.Text: I believe that in both cases it will be a gapped assembly (contigs glued by NNNNNs into scaffolds) and the sequencing reads that are mapped on the assembly to gradually reconstruct what is in the gaps.
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-10T09:52:27.687Z
Answers.LastActivityDate: 2019-04-10T09:52:27.687Z
Answers.UserDisplayName: Kamil S Jaron
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-08T10:11:53.387Z
Comments.Text: Is gap filling for viruses in principle different than gap filling in pro/eukaryotes? I could make some suggestions but they are based on my experience in insect genomics.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-09T23:44:02.540Z
Comments.Text: I don't think it's too different. It's pretty straightforward actually. Virus that I am sequencing does not contain any introns and overlapping ORFs. It has distinct conding regions flanked by promoter sequence in the intergenic region. And I have well annotated reference sequence too. Your suggestion would be really helpful.
Comments.UserDisplayName: LoveVirology
Tags: <genome><assembly><covid-19><sars-cov-2>
Title: Viral genome finishing
ThreadText: # Viral genome finishing
  
  (Asked by: username_0 on 2019-04-06)
  
  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:
  
  1. IMAGE from PAGIT. It asks for ace file which I guess is obtained from Newbler. So, I am not able to use this.
  2. 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?
  
  **Tags:** genome, assembly, covid-19, sars-cov-2
  
  > **Comments:**
  > **username_1**: Is gap filling for viruses in principle different than gap filling in pro/eukaryotes? I could make some suggestions but they are based on my experience in insect genomics.  
  > **username_0**: I don't think it's too different. It's pretty straightforward actually. Virus that I am sequencing does not contain any introns and overlapping ORFs. It has distinct conding regions flanked by promoter sequence in the intergenic region. And I have well annotated reference sequence too. Your suggestion would be really helpful.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-04-10. Score: 2
  
  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](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0663-4) a successor of GapFiller from [ABySS](http://www.bcgsc.ca/platform/bioinfo/software/abyss) package and GapCloser from [SOAPdenovo2](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626529/) 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).
  
  > **Comments:**
  > **username_0**: Can you please tell what input files do Sealer and GapFiller take ?  
  > **username_1**: I believe that in both cases it will be a gapped assembly (contigs glued by NNNNNs into scaffolds) and the sequencing reads that are mapped on the assembly to gradually reconstruct what is in the gaps.  
  
  ---
  
  