3
$\begingroup$

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?

Improve this question
$\endgroup$
2
  • $\begingroup$ 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. $\endgroup$
    – Kamil S Jaron
    Apr 8, 2019 at 10:11
  • $\begingroup$ 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. $\endgroup$
    – L R Joshi
    Apr 9, 2019 at 23:44

1 Answer 1

Reset to default
2
$\begingroup$

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).

Improve this answer
$\endgroup$
2
  • $\begingroup$ Can you please tell what input files do Sealer and GapFiller take ? $\endgroup$
    – L R Joshi
    Apr 10, 2019 at 19:35
  • $\begingroup$ 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. $\endgroup$
    – Kamil S Jaron
    Apr 12, 2019 at 7:59

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.