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kmer analysis for genome size estimation

Hi, I used the PacBio HiFi reads in Merqury/1.9 for kmer analysis of our allotetraploid species. I have shared the figure of genomescope plot, which showing the size of 1.5gb. I am astonished what's wrong here. Can someone guide me in this? For more information, the diploid species has a genome size 1.5 gb. I shall be grateful to you. First, I assembled the genome using hifiasm with size of ~3.7gb.

Second question is why the observed peaks are going out of the model peak?

enter image description here

kmer merqury allotetraploid pacbio hifiasm
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written by rj.rezwan • rj.rezwan

Isn't this size estimate a good fit? I am not sure, but is Ploidy taken into account at all for this? You can also see that dup:4.11 which would fit with tetraploidy. Also, even if there was very high heterozygosity in the genome, this would at best add a fraction of a percent more unique k-mers.

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written by Michael Dondrup Michael Dondrup

yes, this thing want to ask why this does not give a length near to my assembly size? and please look at the observed peak (blue), is this normal to be out of the model peak (black)?

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written by rj.rezwan • rj.rezwan

1 answer

The oh-know materials have all kinds of example plots for various genome cases or extra settings for cases where the size estimation didn't work out. In your case, looks a little bit like the allotetraploid example plot? https://github.com/KamilSJaron/oh-know/wiki/Allotetraploid

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written by Philipp Bayer Philipp Bayer

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