Open Liyong-Zhang opened 3 days ago
Hi there,
I am using GenomeScope2 to check the heterozygosity rate of a plant genome (2n=28) with HiFi reads.
The initial assembly with Hifiasm was used for running a mummerplot with A. thaliana genome as reference, this plant looks like a tetraploid.
The command for checking the heterozygous rate is genomescope.R -i reads_fasta.histo -o ./ -p 4 -k 21 -n "p4"
genomescope.R -i reads_fasta.histo -o ./ -p 4 -k 21 -n "p4"
The results are p4_summary.txt
I have trouble understanding the results. What's the overall heterozygosity rate? 7.85371%?
Also, since the two haplotypes rate (aabc and abcd) are very low aabc 0.001% abcd 0.0121%.
Could I treat this plant as a diploid when using Hifiasm for assembly given that Hifiasm doesn't fully support polyploid genome yet (https://hifiasm.readthedocs.io/en/latest/faq.html#are-polyploid-genomes-supported).
Thank you so much for your help!
Hi there,
I am using GenomeScope2 to check the heterozygosity rate of a plant genome (2n=28) with HiFi reads.
The initial assembly with Hifiasm was used for running a mummerplot with A. thaliana genome as reference, this plant looks like a tetraploid.
The command for checking the heterozygous rate is
genomescope.R -i reads_fasta.histo -o ./ -p 4 -k 21 -n "p4"The results are p4_summary.txt
I have trouble understanding the results. What's the overall heterozygosity rate? 7.85371%?
Also, since the two haplotypes rate (aabc and abcd) are very low aabc 0.001% abcd 0.0121%.
Could I treat this plant as a diploid when using Hifiasm for assembly given that Hifiasm doesn't fully support polyploid genome yet (https://hifiasm.readthedocs.io/en/latest/faq.html#are-polyploid-genomes-supported).
Thank you so much for your help!