https://github.com/cmdcolin/jbrowse-plugin-graphgenomeviewer

A JBrowse 2 graph genome viewer (WIP)
https://github.com/cmdcolin/jbrowse-plugin-graphgenomeviewer

Last synced: 10 months ago
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A JBrowse 2 graph genome viewer (WIP)

• Host: GitHub
• URL: https://github.com/cmdcolin/jbrowse-plugin-graphgenomeviewer
• Owner: cmdcolin
• Created: 2025-01-21T18:22:31.000Z (over 1 year ago)
• Default Branch: master
• Last Pushed: 2025-02-19T17:15:04.000Z (over 1 year ago)
• Last Synced: 2025-07-03T15:09:04.935Z (12 months ago)
• Language: JavaScript
• Size: 16.1 MB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# jbrowse-plugin-graphgenomeviewer

WIP for displaying graph genome as a view in JBrowse 2

## Screenshot

![](img/1.png)

## Concept

The code adds:

- a simple file selector for the user to open .gfa files to display alognside

  the genome browser (these are meant to be locus-specific smallish GFA, not

  full assembly graphs)

- alternatively, can configure a "GFA server" which will use the `vg chunk`

  command to extract the region into a web based bandage-like graph genome

  viewer https://github.com/cmdcolin/graphgenomeviewer

## Thanks

To the StableGenomics team for their PAG workshop helping explain some vg

toolkit commands and concepts https://github.com/StableGenomics/PangPAG

## TODOs

Shortlist of TODOs

- Easier navigation between the linear genome view and graph genome panel

- Ability to launch a synteny-style view from the graph

- Ability to use decompose graph into VCF track

- Ability to show paths/walks

- Debug issue where vg chunk GFA output not loadable in bandage

- Improve scalability

- Bi-directional mouseover from genome to graph and back

- Less chunk-y-ness from the vg chunk graph (?)