Answers.Body: <p>To construct a pangenome that can be used as reference for the assembly of organisms of the same specie I used the <a href="https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md" rel="nofollow noreferrer">Minigraph-Cactus pipeline</a> which also has a very clear tutorial using Yeast genomic data.
  It is useful for your purpose and pangenomes from Minigraph-Cactus are indexable for and ready for read mapping with vg Giraffe since it also can output <code>.gbz</code>, <code>.dist</code> and <code>.min</code> files.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-05-27T16:27:01.850Z
Answers.LastActivityDate: 2024-05-27T16:27:01.850Z
Answers.UserDisplayName: AIsaac
Body: <p>I am working with yeast strains (specifically S. cerevisiae) that have been cultured and evolved over many generations in the lab. I am using the reference S288C strain when I do certain analyses but I want to be able to construct my own reference using the &quot;in-house&quot; strains. Ultimately I want to be able to call variants when mapping strains to this &quot;in-house&quot; reference to make it easier to visualize/understand the difference in strains.</p>
  <p>I am trying to use <a href="https://github.com/vgteam/vg" rel="nofollow noreferrer">VG-tools</a> to create a pangenome graph using 10 different strains all sharing the same reference and I'm honestly a little confused on how to go about doing it. I was able to make a &quot;vg&quot; file for each sample individually but I know downstream I want to be able to map other strains to this pangenome as a reference and call variants to it rather than the standard reference sequence.</p>
  <p>I'm mainly looking to see if anyone has built a &quot;pangenome graph&quot; using multiple samples and how they went about doing it. If anyone could give me some tips/tricks/advice for this kind of task that would be great!</p>
  <p>I have a phylogenetic tree of all the strains but how would I use that to see the differences in variation?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-27T18:18:31.613Z
Comments.Text: Hi @rimo what do you mean by a "graph". In graph theory a "graph" is a network. If its a classical bivariate plot, what is the y-axis? Finally, what about simply doing a tree?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-27T18:35:17.653Z
Comments.Text: Could you post a tree - remove the taxa labels to ensure confidentiality - and I will tell you how to read it. The answer is in the tree. Where the SNPs are located is a different analysis BTW.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-29T03:47:10.020Z
Comments.Text: @M__ rimo is talking about a genome graph, like the example shown in the [vg repository](https://github.com/vgteam/vg#variation-graph-data-structures-interchange-formats-alignment-genotyping-and-variant-calling-methods)
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-07-29T04:25:31.500Z
Comments.Text: @gringer I did raise this point originally. This is graph theory, but graph theory is based on trees (it provides the direction).
Comments.UserDisplayName: M__
Tags: <reference-genome><graphs><pangenome>
Title: Constructing a pangenome graph using multiple samples
ThreadText: # Constructing a pangenome graph using multiple samples
  
  (Asked by: username_0 on 2023-07-27)
  
  I am working with yeast strains (specifically S. cerevisiae) that have been cultured and evolved over many generations in the lab. I am using the reference S288C strain when I do certain analyses but I want to be able to construct my own reference using the "in-house" strains. Ultimately I want to be able to call variants when mapping strains to this "in-house" reference to make it easier to visualize/understand the difference in strains.
  
  I am trying to use [VG-tools](https://github.com/vgteam/vg) to create a pangenome graph using 10 different strains all sharing the same reference and I'm honestly a little confused on how to go about doing it. I was able to make a "vg" file for each sample individually but I know downstream I want to be able to map other strains to this pangenome as a reference and call variants to it rather than the standard reference sequence.
  
  I'm mainly looking to see if anyone has built a "pangenome graph" using multiple samples and how they went about doing it. If anyone could give me some tips/tricks/advice for this kind of task that would be great!
  
  I have a phylogenetic tree of all the strains but how would I use that to see the differences in variation?
  
  **Tags:** reference-genome, graphs, pangenome
  
  > **Comments:**
  > **username_1**: Hi @username_0 what do you mean by a "graph". In graph theory a "graph" is a network. If its a classical bivariate plot, what is the y-axis? Finally, what about simply doing a tree?  
  > **username_1**: Could you post a tree - remove the taxa labels to ensure confidentiality - and I will tell you how to read it. The answer is in the tree. Where the SNPs are located is a different analysis BTW.  
  > **username_2**: @username_1 username_0 is talking about a genome graph, like the example shown in the [vg repository](https://github.com/vgteam/vg#variation-graph-data-structures-interchange-formats-alignment-genotyping-and-variant-calling-methods)  
  > **username_1**: @username_2 I did raise this point originally. This is graph theory, but graph theory is based on trees (it provides the direction).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2024-05-27. Score: 1
  
  To construct a pangenome that can be used as reference for the assembly of organisms of the same specie I used the [Minigraph-Cactus pipeline](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md) which also has a very clear tutorial using Yeast genomic data.
  It is useful for your purpose and pangenomes from Minigraph-Cactus are indexable for and ready for read mapping with vg Giraffe since it also can output `.gbz`, `.dist` and `.min` files.
  
  
  ---
  
  