Linking pggb output to Panache input

SouthGreenPlatform / panache

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

MIT License

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Linking pggb output to Panache input #38

Open SingingMeerkat opened 3 months ago

SingingMeerkat commented 3 months ago

Interest have been expressed about visualizing graphs from pggb into Panache ( cf nf-core/pangenome#197), but the steps to convert formats are currently unclear.

Some documentation highlighting how to convert pggb's output into Panache's input would be welcome.

I cannot dedicate much time to it right now, but maybe that's something that @francoissabot can look into? I at least create the issue to look into it later.

francoissabot commented 3 months ago

We have a prototype for GFA parser in a PAV matrix, will see if we can adapt it. Normally it will work for PGGB as well as for Mningraph/Cactus and GFA1.1 formats