I used PacBio HiFi data (17 Gbp) to assess the genome size of a diploid fungus.
First, I used KMC to get the histo data (k=21), then I used Genomescope 2.0 for evaluation and visualization.
My input commands are as follows:
kmc -k21 -t32 -m64 -ci1 -cs1000000 @HCSR214 HCSR214.KMC21.cs1000000 tmp/kmc_tools transform $SAMPLE.21.kmc histogram HCSR214.KMC21.cs1000000.hist -cx1000000
But the result seems to have some problems because of the low model fit.
Hello Mike,
Thanks for developing this amazing software!
I used PacBio HiFi data (17 Gbp) to assess the genome size of a diploid fungus. First, I used KMC to get the histo data (k=21), then I used Genomescope 2.0 for evaluation and visualization. My input commands are as follows:
kmc -k21 -t32 -m64 -ci1 -cs1000000 @HCSR214 HCSR214.KMC21.cs1000000 tmp/kmc_tools transform $SAMPLE.21.kmc histogram HCSR214.KMC21.cs1000000.hist -cx1000000But the result seems to have some problems because of the low model fit.Here's the output of my result. http://genomescope.org/genomescope2.0/analysis.php?code=gzgzNA88D0xGsxfJLwAP
Could you please give me some advice on how to fit the model properly? Thank you for your attention!
Best regards, Lucia