Extract bubbles in pangenome graph

Question

[polag01]

Sorry if this has been answered somewhere (although I have searched but found no similar post) or directed to the wrong channel.

I created a pangenome graph using PGGB and would like to extract the regions with bubbles for further analysis. I tried using {gfatools bubble file.gfa} but the command returned an empty file. Is there a different approach or tool to carry out this task?

Thank you in advance.

Answer 1

[colindaven]

• There are a couple of nice methods within the odgi toolkit for SV or PAV detection. https://odgi.readthedocs.io/en/latest/rst/tutorials/presence_absence_variants.html
• If the visualization is insufficient for you also look at Seqtubemap https://github.com/vgteam/sequenceTubeMap
• More on pangenomes in general - https://github.com/colindaven/awesome-pangenomes