Body: <p>I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, Duplications, Inverted regions in my Query sequence on the Y-axis (PacBio Hifi) compared to the reference genome.</p>
  <p>I want to check if these structural variations are real or only resulting from sequencing errors or not. So, I want to manually curate the PacBio assembly. Because I can see at which contig the structural variations are.</p>
  <p>Can you please suggest any tools for manual curation of a genome assembly to investigate whether these structural variations are sequencing errors or real sequence variation?</p>
  <p>I have uploaded the dot-plot below. Thank you.<a href="https://i.sstatic.net/owOVb.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/owOVb.jpg" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-27T20:46:06.370Z
Comments.Text: based on your other question, I would suggest mapping the hi-c reads to this assembly and manually polishing in juicebox
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-28T09:16:52.013Z
Comments.Text: So, you mean take the HiFi fasta and map the Hi-C fasta on it? Or do I need raw reads from the Hi-C reads?
Comments.UserDisplayName: Anik Dutta
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-28T17:41:05.517Z
Comments.Text: You would need to map the raw Hi-C reads. the FASTA is the outcome of a lot of procedures that remove information. It is the Hi-C reads have the actual proximity information about which regions are close to each other on the chromosome. You can use that to correct structural errors (if any). If those are truly errors then they will look weird on the Hi-C heatmap and you can correct them manually in juicebox: https://aidenlab.gitbook.io/juicebox/assembly-tools
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-01-28T18:16:20.233Z
Comments.Text: Ah ok. Thanks for clarifying the confusion. It is clear now.
Comments.UserDisplayName: Anik Dutta
Tags: <genome><assembly><reference-genome><structural-variation><pacbio>
Title: How to manually curate a genome assembly for sequence variation or error?
ThreadText: # How to manually curate a genome assembly for sequence variation or error?
  
  (Asked by: username_0 on 2022-01-27)
  
  I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, Duplications, Inverted regions in my Query sequence on the Y-axis (PacBio Hifi) compared to the reference genome.
  
  I want to check if these structural variations are real or only resulting from sequencing errors or not. So, I want to manually curate the PacBio assembly. Because I can see at which contig the structural variations are.
  
  Can you please suggest any tools for manual curation of a genome assembly to investigate whether these structural variations are sequencing errors or real sequence variation?
  
  I have uploaded the dot-plot below. Thank you.[![enter image description here](https://i.sstatic.net/owOVb.jpg)](https://i.sstatic.net/owOVb.jpg)
  
  **Tags:** genome, assembly, reference-genome, structural-variation, pacbio
  
  > **Comments:**
  > **username_1**: based on your other question, I would suggest mapping the hi-c reads to this assembly and manually polishing in juicebox  
  > **username_0**: So, you mean take the HiFi fasta and map the Hi-C fasta on it? Or do I need raw reads from the Hi-C reads?  
  > **username_1**: You would need to map the raw Hi-C reads. the FASTA is the outcome of a lot of procedures that remove information. It is the Hi-C reads have the actual proximity information about which regions are close to each other on the chromosome. You can use that to correct structural errors (if any). If those are truly errors then they will look weird on the Hi-C heatmap and you can correct them manually in juicebox: https://aidenlab.gitbook.io/juicebox/assembly-tools  
  > **username_0**: Ah ok. Thanks for clarifying the confusion. It is clear now.  
  
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  ## 0 answers
  
  