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ekg / seqwish

alignment to variation graph inducer
MIT License
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interpretation of bacteria pangenome graphs #123

Open jianshu93 opened 3 weeks ago

jianshu93 commented 3 weeks ago

Dear seqwish team,

I built a bacteria pangenome graph with wfmash+seqwish+bandage, which is from Chlamydia trachomatis species, about 50 genomes/strains with ANI> 99%, I have the attached graph output. Does this indicate that those genomes almost do not have rearrangement but there might be a genomic island there (the hollow hole) for some of the genomes (~40%) and some insertion at the bottom for only a few genomes, the plasmid has some structural difference and some insertions but overall are very similar for all genomes. I was just trying to get some biological information out of the pangenome graph that cannot be easily detected without it.

Thanks,

Jianshu

Chlamydia_trachomatis_strain_SQ19

ZoeYang2020 commented 5 days ago

Hi Jianshu, The graph you presented here looks really interesting. I think your interpretation makes sense. Have you tried deconstructing the graph into VCF to check those variations?

jianshu93 commented 5 days ago

Hi @ZoeYang2020, How do I deconstruct the graph to have VCF? New to this but I am extremely interested in exploring the VCF files to study those variations.

Best,

Jianshu