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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Question about pangenome building in species with high level of large translocations #1508

Open GabrieleRigano99 opened 4 weeks ago

GabrieleRigano99 commented 4 weeks ago

First of all, I'd like to thank you for the amazing work done! Secondly, I'm working on a fungal species with very high levels of chromosomal polymorphism and large translocations (of Mbp), and I already built a pangenome using t2t gapless genome assemblies of 11 strains without dividing them by chromosome. I was wondering if it would be possible (and correct) to build a new pangenome graph using also contig or scaffold-level assemblies. If that's the case, should I only use assemblies without gaps or Ns to avoid introducing false haplotypes in the graph? Thank you!

glennhickey commented 3 weeks ago

The --noSplit option (to support inter-chromosome alignments) remains fairly experimental. I don't think there's anything stopping your from trying to add contig and scaffold assemblies, but I unfortunately can't really predict how many errors they will introduce. Please do be careful about interpreting the results if you do use them

GabrieleRigano99 commented 3 weeks ago

thank you very much for the quick reply! I'll keep this in mind then