Question: Estimate the genome heterozygosity from a PacBio dataset
0
gravatar for gabri
21 months 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 • 928 views
ADD COMMENTlink modified 21 months ago by Istvan Albert ♦♦ 80k • written 21 months ago by gabri50
1
gravatar for Istvan Albert
21 months ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k 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 21 months ago by Istvan Albert ♦♦ 80k

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

ADD REPLYlink written 21 months ago by gabri50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 824 users visited in the last hour