Oxford Nanopore for structural variation calling
Hello Biostars!
Just a quick question in the hopes someone might have a general "rule-of-thumb" answer - is there a recommended coverage for Oxford Nanopore for structural variation calling in polyploids? Thanks!
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You had me at "in polyploids". For humans 10-20x is sufficient, although sensitivity increases further with more and longer reads.
We routinely use ~30X for various plants and animals. It becomes really hard to find SVs in centromere and repeats. No experience with polyploids, though. How divergent are the sub-genomes? It is a quite important measure for your analysis.
Hmmm... I don't think the divergence has been estimated yet, the plant's been sequenced about two years ago.
Usually non-coding regions diverge pretty fast after two genomes come together. My hypothesis is (I haven't done any assembly work for polyploids): if it is an ancient (allo-?)polyploid, the non-genic region would be divergent enough so you wouldn't have trouble in assembly process with long reads. If the sub-genomes are very close and have not diverged a lot, the assembly becomes much harder.