Answers.Body: <p>I would suggest making a <a href="https://dgenies.toulouse.inra.fr/" rel="nofollow noreferrer">dot plot of your assembly</a> against a reference (related) yeast genome assembly.</p>
  <p>I'd suggest also running <a href="https://github.com/ablab/quast" rel="nofollow noreferrer">QUAST</a> against the yeast reference to get a finer grained idea of the comparison.</p>
  <p>Bandage is more of an assembly QC tool for understanding whether there are issues with the assembly. It will not tell you anything about ploidy or that kind of thing.</p>
  <p>Off the top of my head, I find it worrisome that 90% of your sequence is in a single scaffold/contig. Presumably there's more than a single chromosome. It does look like the repeats are messing you up.</p>
  <p>I'd suggest using <a href="https://github.com/chhylp123/hifiasm" rel="nofollow noreferrer">hifiasm</a> instead and seeing if it makes different decisions.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-25T21:21:53.853Z
Answers.LastActivityDate: 2023-08-25T21:21:53.853Z
Answers.UserDisplayName: Maximilian Press
Body: <p>I assembled Nanopore sequenced reads with Flye and visualized the GFA graph in Bandage but I don't really know how to interpret the result. For context, this is a yeast (DNA) genome. My goal is to figure out areas of repeats, ploidy level, and overall structure of the strain. So far I understand that the bubbles are repetitive areas but I mainly want to know how to interpret a graph like this.</p>
  <p><a href="https://i.sstatic.net/4EART.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/4EART.png" alt="enter image description here" /></a></p>
  <p>I'm new to interpreting these graphs and I couldn't find any sort of guide online so if someone has any resources they'd be willing to share or if they could help interpret this graph I would really appreciate it!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-10T17:17:07.043Z
Comments.Text: Please [edit] your question and add some detail. To be honest, I don't have a clue what this is, I've never seen this sort of thing before, so your question might be clearer to someone who knows more, but adding some detail can't hurt. For example, what organism did you sequence? What kind of sequencing (RNA? DNA?). Also, why did you plot the GFA? What question are you asking of your data?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-08-14T05:39:59.387Z
Comments.Text: I've used Bandage to visualise transcriptome assemblies, but I'm not sure how to answer your question/s about repeats, ploidy, and structure sorry. If you don't get an answer here, I suggest reaching out to the author - Ryan Wick (email: ryan.wick@unimelb.edu.au / mastodon: @rrwick@genomic.social / github: https://github.com/rrwick/). Good luck!
Comments.UserDisplayName: jared_mamrot
Tags: <assembly>
Title: Interpreting GFA graph visualized in Bandage
ThreadText: # Interpreting GFA graph visualized in Bandage
  
  (Asked by: username_0 on 2023-08-10)
  
  I assembled Nanopore sequenced reads with Flye and visualized the GFA graph in Bandage but I don't really know how to interpret the result. For context, this is a yeast (DNA) genome. My goal is to figure out areas of repeats, ploidy level, and overall structure of the strain. So far I understand that the bubbles are repetitive areas but I mainly want to know how to interpret a graph like this.
  
  [![enter image description here](https://i.sstatic.net/4EART.png)](https://i.sstatic.net/4EART.png)
  
  I'm new to interpreting these graphs and I couldn't find any sort of guide online so if someone has any resources they'd be willing to share or if they could help interpret this graph I would really appreciate it!
  
  **Tags:** assembly
  
  > **Comments:**
  > **username_1**: Please [edit] your question and add some detail. To be honest, I don't have a clue what this is, I've never seen this sort of thing before, so your question might be clearer to someone who knows more, but adding some detail can't hurt. For example, what organism did you sequence? What kind of sequencing (RNA? DNA?). Also, why did you plot the GFA? What question are you asking of your data?  
  > **username_2**: I've used Bandage to visualise transcriptome assemblies, but I'm not sure how to answer your question/s about repeats, ploidy, and structure sorry. If you don't get an answer here, I suggest reaching out to the author - Ryan Wick (email: ryan.wick@unimelb.edu.au / mastodon: @rrwick@genomic.social / github: https://github.com/rrwick/). Good luck!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-08-25. Score: 1
  
  I would suggest making a [dot plot of your assembly](https://dgenies.toulouse.inra.fr/) against a reference (related) yeast genome assembly.
  
  I'd suggest also running [QUAST](https://github.com/ablab/quast) against the yeast reference to get a finer grained idea of the comparison.
  
  Bandage is more of an assembly QC tool for understanding whether there are issues with the assembly. It will not tell you anything about ploidy or that kind of thing.
  
  Off the top of my head, I find it worrisome that 90% of your sequence is in a single scaffold/contig. Presumably there's more than a single chromosome. It does look like the repeats are messing you up.
  
  I'd suggest using [hifiasm](https://github.com/chhylp123/hifiasm) instead and seeing if it makes different decisions.
  
  
  ---
  
  