Estimate the genome heterozygosity from a PacBio dataset

Question

[gabri]

Hi!

I know that in the case of Illumina sequences it is possible to use jellyfish for the k-mers count, using short sequences and the same length. I would like to know if there is a method / software to estimate the genome heterozygosity from a PacBio dataset. Is jellyfish equally correct?

Thank you!

Answer 1

[Istvan Albert]

I would say that considering the high error rates of PacBio you can only hope such a method to work if your PacBio run was set up to produce shorter and higher quality consensus sequences. Even then you would need fairly high coverage.

[gabri]

Thanks a lot for the answer! This is a very useful advice.