<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>

CC BY-SA 4.0
2019-04-10T19:35:38.223Z
Can you please tell what input files do Sealer and GapFiller take ?
LoveVirology
CC BY-SA 4.0
2019-04-12T07:59:21.667Z
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.
Kamil S Jaron
CC BY-SA 4.0
2019-04-10T09:52:27.687Z
2019-04-10T09:52:27.687Z
Kamil S Jaron
<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>

CC BY-SA 4.0
2019-04-08T10:11:53.387Z
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.
Kamil S Jaron
CC BY-SA 4.0
2019-04-09T23:44:02.540Z
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.
LoveVirology
<genome><assembly><covid-19><sars-cov-2>
Viral genome finishing
# 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.  

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## 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.  

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