Visualizing pangenome graphs about pggb HOT 2 CLOSED

If I understood Pandora correctly, it can break down the resulting pangenome into a VCF.
If so, I would suggest creating a variation graph using vg construct https://github.com/vgteam/vg with the FASTA reference and the VCF from Pandora. Translate it into GFA using vg view.
Then use odgi build and subsequently odgi viz to create a 1D visualization of your pangenome. odgi layout and odgi draw can render a 2D visualization of the pangenome. However, it might help to normalize your pangenome first using smoothxg.

If you are looking for interactive visualization methods of pangenomes in the GFA format, you can also take a look at
https://github.com/MoMI-G/MoMI-G/ which is great for the interactive visualization of reference centered pangenomes. Or https://github.com/vgteam/sequenceTubeMap. There is also https://rrwick.github.io/Bandage/ or https://github.com/ggonnella/gfaviz for interactive 2D visualizations. Pantograph https://graph-genome.github.io/ tries to be an interactive version of the odgi viz 1D visualization, but might not scale well enough. Depends on the pangenome size.
You can find a summary of visualization tools for pangenome graphs in section 6.1 of https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-120219-080406.

I hope this helps!

from pggb.

Thank you so much for your detailed guidance! I will take a look at all of those!

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