WGS for CNV and Aneuploidy analysis

Question

[bioinfo1990]

Hello, I’m planning to run whole genome sequencing on sheep cells for CNV and aneuploidy analysis. I’m wondering what sequencing depth is typically recommended, how many million reads I should ask for, and what read length would be ideal. While this project involves sheep, I’d love to hear any general rules of thumb for different genome sizes. Also, if you have any tool recommendations for this kind of analysis, I’m all ears. Thank you.

[colindaven]

"how many million cells" - are you talking WGS or single cell scWGS ?

[GenoMax]

While you wait for answers this should get to started: https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-023-01703-8
https://humgenomics.biomedcentral.com/articles/10.1186/s40246-021-00332-5

These are human samples so you will have to extrapolate to sheep based on your own domain knowledge.