some questions about svtigs

[wjwei-handsome]

Hi @asylvz , svtigs is a cool representation, but I still have some questions about it:

how to get the breakpoints or call variants? My process is aligning svtigs.fa to ref.fa, so that I could get the variants of ref.

But how about the non-reference path? After got the variants of some_path, how to augment the original graph by using this non-reference variants ?

Sincerely Looking forward to your answer :D

Best regards,
Wenjie

[asylvz]

You are right, if your reference does not have the related alternative sequences, then you can't find the non-reference breakpoints. This is the drawback of linear refs.

About augmentation, I don't know of any specific algorithm but here (https://www.biorxiv.org/content/10.1101/2024.04.18.590093v1.abstract), we use a pipeline to augment the graph. You can check this. Another alternative might be VG (https://github.com/vgteam/vg). They have graph augmentation as far as I know, but I'm not sure if it will work in your case.

[wjwei-handsome]

what do you think about that fill svtigs.fa to original graph ?

[asylvz]

I couldn't understand what you mean?

[wjwei-handsome]

sorry, what I mean is that augment the original graph by svitg.fa

minigraph -cxggs <svtig.fa> -o < augmented.gfa>