Extract bubbles in pangenome graph
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.
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colindaven
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polag01 •
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polag01 •
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- 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
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