Answers.Body: <p>the cactus docs talk about visualization here <a href="https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#visualization" rel="nofollow noreferrer">https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#visualization</a></p>
  <p>I also collect visualization tools and these are the ones i have tagged as &quot;graph&quot; <a href="https://cmdcolin.github.io/awesome-genome-visualization/?language=&amp;tag=Graph&amp;platform=&amp;latest=true" rel="nofollow noreferrer">https://cmdcolin.github.io/awesome-genome-visualization/?language=&amp;tag=Graph&amp;platform=&amp;latest=true</a> and ones i have tagged as &quot;pangenome&quot; <a href="https://cmdcolin.github.io/awesome-genome-visualization/?language=&amp;tag=Pangenome&amp;platform=&amp;latest=true" rel="nofollow noreferrer">https://cmdcolin.github.io/awesome-genome-visualization/?language=&amp;tag=Pangenome&amp;platform=&amp;latest=true</a></p>
  <p>I see specifically that you refer to conservation. panagram was a tool that was presented that actually does a very nice way of showing conservation by k-mers. it is not graph based, but k-mer based <a href="https://github.com/kjenike/panagram" rel="nofollow noreferrer">https://github.com/kjenike/panagram</a> (presentation <a href="https://www.dropbox.com/s/g7snjgr8bs6c2uj/2023.01.17.Panagram.pdf" rel="nofollow noreferrer">https://www.dropbox.com/s/g7snjgr8bs6c2uj/2023.01.17.Panagram.pdf</a>). other tools you see on posters a lot also include syri/plotsr <a href="https://schneebergerlab.github.io/syri/" rel="nofollow noreferrer">https://schneebergerlab.github.io/syri/</a> and GENESPACE.</p>
  <p>this is also of course a relatively new field, so, you might also make your own tools/visualizations for the purpose (and share them back with us!)</p>
  
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Answers.Body: <p>One additional option that I'll mention is anvi'o (scroll down to the figures to see if it's something you might be interested in <a href="https://merenlab.org/2016/11/08/pangenomics-v2/" rel="nofollow noreferrer">https://merenlab.org/2016/11/08/pangenomics-v2/</a> ).</p>
  
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Answers.Text: I've been spending some time to go through anvi'o documentation and it seems a very interesting tool but not exactly useful for my purpose.
  I want to focus on the visualization of a pangenome constructed with the cactus pipeline that is able to create a single pangenome graph and my aim is to use it as reference for assembly of other organisms of the same specie. Therefore I just need to visualize its structure to better understand if there are big issues with it before starting evaluating the mapping performances.
  As far as I understood anvi'o focus on comparative genomics.
  But thank you!
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Answers.Body: <p>Unfortunately, this is still kind of an open problem. However, recently this tool is being developed and it's extremely promissing, but it's still under development. It is called <a href="https://github.com/qwx9/strangepg" rel="nofollow noreferrer"><code>strangepg</code></a>
  There is also <a href="https://github.com/rrwick/Bandage" rel="nofollow noreferrer"><code>Bandage</code></a> and <a href="https://github.com/asl/BandageNG" rel="nofollow noreferrer"><code>BandageNG</code></a></p>
  <p>However, with the size of your graph, I doubt any of them can visualize such graph. Therefore, I would advice you first to split it into separate components, you can do this with this tool <a href="https://github.com/fawaz-dabbaghieh/gfa_subgraphs" rel="nofollow noreferrer"><code>GFASubgraphs</code></a>. This will output each component into a separate GFA file and you can maybe visualize each individually.</p>
  
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Body: <p>I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most of them are related to prokaryotic genomes (which are smaller size) and/or chunks of eukaryotic genomes to study specific haplotypes.
  My pangenome has these characteristics:</p>
  <pre><code>nodes   18424540
  edges   24616683
  length  1069101379
  </code></pre>
  <p>My objective is to be able to get an image of the full pangenome or one for each chromosome, from which has to be possible to interpret approximatevly its structure and where significant divergence between the genome sequences is found.</p>
  <p>So far the programs I have been using were not able to give a meaningful image of the eukaryotic pangenome in question.</p>
  <p>I come here to ask if anyone has found him/herself in this situation before, and if you manage to find a solution or even a compromise to still be able to have an idea of its structure indirectly, it would be very much of help for me!</p>
  <p>Thank you in advance</p>
  <p>My pangenome has been created following the Cactus pipeline step-by-step (skipping the optional 3rd step).</p>
  
Tags: <genome><visualization><reference-genome><graphs><pangenome>
Title: Are there efficient tools for PANGENOMES visualization (GFA size >2GB)?
ThreadText: # Are there efficient tools for PANGENOMES visualization (GFA size >2GB)?
  
  (Asked by: username_0 on 2024-05-27)
  
  I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most of them are related to prokaryotic genomes (which are smaller size) and/or chunks of eukaryotic genomes to study specific haplotypes.
  My pangenome has these characteristics:
  
  ```
  nodes   18424540
  edges   24616683
  length  1069101379
  
  ```
  
  My objective is to be able to get an image of the full pangenome or one for each chromosome, from which has to be possible to interpret approximatevly its structure and where significant divergence between the genome sequences is found.
  
  So far the programs I have been using were not able to give a meaningful image of the eukaryotic pangenome in question.
  
  I come here to ask if anyone has found him/herself in this situation before, and if you manage to find a solution or even a compromise to still be able to have an idea of its structure indirectly, it would be very much of help for me!
  
  Thank you in advance
  
  My pangenome has been created following the Cactus pipeline step-by-step (skipping the optional 3rd step).
  
  **Tags:** genome, visualization, reference-genome, graphs, pangenome
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2024-05-28. Score: 2 | Accepted answer
  
  the cactus docs talk about visualization here <https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#visualization>
  
  I also collect visualization tools and these are the ones i have tagged as "graph" <https://cmdcolin.github.io/awesome-genome-visualization/?language=&tag=Graph&platform=&latest=true> and ones i have tagged as "pangenome" <https://cmdcolin.github.io/awesome-genome-visualization/?language=&tag=Pangenome&platform=&latest=true>
  
  I see specifically that you refer to conservation. panagram was a tool that was presented that actually does a very nice way of showing conservation by k-mers. it is not graph based, but k-mer based <https://github.com/kjenike/panagram> (presentation <https://www.dropbox.com/s/g7snjgr8bs6c2uj/2023.01.17.Panagram.pdf>). other tools you see on posters a lot also include syri/plotsr <https://schneebergerlab.github.io/syri/> and GENESPACE.
  
  this is also of course a relatively new field, so, you might also make your own tools/visualizations for the purpose (and share them back with us!)
  
  
  ---
  
  ### Answer by username_2 on 2024-05-28. Score: 2
  
  One additional option that I'll mention is anvi'o (scroll down to the figures to see if it's something you might be interested in <https://merenlab.org/2016/11/08/pangenomics-v2/> ).
  
  > **Comments:**
  > **username_0**: I've been spending some time to go through anvi'o documentation and it seems a very interesting tool but not exactly useful for my purpose. I want to focus on the visualization of a pangenome constructed with the cactus pipeline that is able to create a single pangenome graph and my aim is to use it as reference for assembly of other organisms of the same specie. Therefore I just need to visualize its structure to better understand if there are big issues with it before starting evaluating the mapping performances. As far as I understood anvi'o focus on comparative genomics. But thank you!  
  
  ---
  
  ### Answer by username_3 on 2024-11-27. Score: 2
  
  Unfortunately, this is still kind of an open problem. However, recently this tool is being developed and it's extremely promissing, but it's still under development. It is called [`strangepg`](https://github.com/qwx9/strangepg)
  There is also [`Bandage`](https://github.com/rrwick/Bandage) and [`BandageNG`](https://github.com/asl/BandageNG)
  
  However, with the size of your graph, I doubt any of them can visualize such graph. Therefore, I would advice you first to split it into separate components, you can do this with this tool [`GFASubgraphs`](https://github.com/fawaz-dabbaghieh/gfa_subgraphs). This will output each component into a separate GFA file and you can maybe visualize each individually.
  
  
  ---
  
  