significant differences of genome size estimates when varying the Max kmer coverage about genomescope HOT 2 OPEN

Hello, thanks for using GenomeScope!

Is it possible that the bivalve species you are analyzing is not diploid? Looking at your histogram, I am wondering there is a possibility that it is tetraploid. We will soon release a version of GenomeScope that works for polyploid organisms. I analyzed your histogram using the new version of GenomeScope with a tetraploid model, and I was able to get a better convergence. See the plot below:

The estimated genome size is 1.176 Gbp (this is the genome size for a single copy of the chromosomes, the tetraploid genome size would be 4 times this size). You can also see the estimated heterozygosity values in the plot, where aaaa refers the the percentage of locations along the polyploid genome where the four nucleotides are the same, abcd refers to the percentage of locations where they are all different, etc.

Let me know if you have any further questions.

from genomescope.

Hello,

Thanks so much for that, looking forward to the new version.

We don't have the karyotype of the actual specimen sequenced but we know that the karyotype of that species is diploid.

Thanks
Jorge

from genomescope.