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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Does minigraph build genome graph including structural variants from a SV caller? #22

Open clairemerot opened 3 years ago

clairemerot commented 3 years ago

Hello, I'm also keen to integrate into the genome graph the structural variability detected by Sv callers (from short reads and/or long-reads). I was wondering if minigraph handles that? Those are often represented in a vcf which some programs can integrate into a genome-graph. I am using vg at the moment (https://github.com/vgteam/vg) which is fast at constructing the graph but slow at mapping. Hence, we are super interested in using minigraph, as it seems to be very efficient (and I remember the efficiency of minimap!). I may also have a second reference assembly so the idea in the end would be to build a graph integrating several assemblies and local SV; Thank you for your help and attention, Claire

cistarsa commented 3 years ago

I am also attempting this, did you figure this out?

lh3 commented 3 years ago

No, minigraph doesn't do that. To a large extent, minigraph itself is a SV caller for long contigs.

clairemerot commented 3 years ago

Thanks for your reply, And thanks a lot the addition in the readme about SV-calling with minigraph, I'm trying that, as I have two assemblies to compare!

I was wondering whether it would be possible (and would make sense), to build a graph with two assemblies in minigraph, to get a good basis of pangenome graph, and then export the gfa to enrich it with more SVs (likely shorter ones inferred from larger sample sizes) in other software like vg? anyone has tried that?

Cheers Claire