Question: Estimate the genome heterozygosity from a PacBio dataset
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gravatar for gabri
2.5 years ago by
gabri50
gabri50 wrote:

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!

heterozygosity pacbio genome • 1.2k views
ADD COMMENTlink modified 2.5 years ago by Istvan Albert ♦♦ 82k • written 2.5 years ago by gabri50
1
gravatar for Istvan Albert
2.5 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

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.

ADD COMMENTlink written 2.5 years ago by Istvan Albert ♦♦ 82k

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

ADD REPLYlink written 2.5 years ago by gabri50
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