Question: Graph size restrictions to what vg viz can visualise?
0
gravatar for LilithElina
12 months ago by
LilithElina10
Germany
LilithElina10 wrote:

Hi!

I like the way vg viz visualises the variant graph, but it seems I arrived at a point where it's not working anymore... I have a grpah constructed with seqwish from five whole bacterial genomes. Converting to VG format and creating an XG index worked just fine, but the SVG created by vg viz is empty. Is tehre a limit to what this tool can do, or is it a different problem somehow?

Thanks in advance,
Sarah

vg • 256 views
ADD COMMENTlink written 12 months ago by LilithElina10

Sorry no idea. I've read vg viz can produce blank files if the paths are large. It's been suggested to use bandage instead. I think you should post an issue on github about it.

ADD REPLYlink modified 12 months ago • written 12 months ago by Mark800

Thank you! That was exactly what I was thinking, I just couldn't find any reference to it. If you've read somewhere that vg viz can produce blank files for large paths I have my answer.

ADD REPLYlink written 12 months ago by LilithElina10
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