Biostar Beta. Not for public use.
Oxford Nanopore for structural variation calling
0
Entering edit mode
15 months ago
borealis • 20

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!

ADD COMMENTlink
1
Entering edit mode

You had me at "in polyploids". For humans 10-20x is sufficient, although sensitivity increases further with more and longer reads.

ADD REPLYlink
1
Entering edit mode

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.

ADD REPLYlink
0
Entering edit mode

Hmmm... I don't think the divergence has been estimated yet, the plant's been sequenced about two years ago.

ADD REPLYlink
1
Entering edit mode

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.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1