jbrowse-plugin-graphgenomeviewer v1.0.1

jbrowse-plugin-graphgenomeviewer

WIP for displaying graph genome as a view in JBrowse 2

Screenshot

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 (?)