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how to make the correct genome size estimation for allotetraploid species? #634
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How did you run hifiasm? A good k-mer plot should be: https://hifiasm.readthedocs.io/en/latest/faq.html#why-does-hifiasm-stuck-or-crash. If only primary assembly is required, you could have a try to run purge_dups after hifiasm assemmbly. |
Sorry for the late reply because I was traveling and busy with field experiment. I used these commands for the assembly #1st command
output
#2nd command
output
I used 1st command output file for making kmer analysis with merqury. Please check the result and let me know some great suggestions. Moreover, I want to add here that the parents of polyploid species have high homology. |
Hi, I assembled the genome of allotetraploid species using hifiasm with size of ~3.7gb. I used the PacBio HiFi reads in Merqury for kmer analysis of genome estimation 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?
Second question is why the observed peaks are going out of the model peak? I shall be grateful to you.
Regards
Rezwan
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