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pangenome / odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
https://doi.org/10.1093/bioinformatics/btac308
MIT License
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W lines and P lines - visualizing output from cactus pangenome pipeline #437

Closed agolicz closed 2 years ago

agolicz commented 2 years ago

Hi, I've built a graph with cactus pangenome pipeline and wanted to visually compare with pggb using odgi viz. However, in the cactus pipeline, other than the reference contigs paths stored as P-lines all other paths are listed as haplotype threads (W-lines). But it looks like these are not visualized as paths by odg viz. Is there a quick way to convert W-lines to P-lines? Thanks! Agnieszka

Cactus pangenome pipeline output: https://get.massive.app/01G9F4NMSDQR3A0TCD1FZ4A1Q9?secret=hfGzIuSGFpDIOHnB

agolicz commented 2 years ago

Looks like I might have found my answer... I'll try https://github.com/pangenome/gfa-wp

agolicz commented 2 years ago

Yep, works!

AndreaGuarracino commented 2 years ago

image

agolicz commented 2 years ago

Oh my childhood favorite :P. Thanks anyways, I'm sure I'll be back!