How I know the genome assembly quality by the low coverage Pacbio data ?

Question

[wdpang]

Hi,

I have finished the assembly genome, and i have a low average Pacbio data. I want to estimate the quality of the result. So, i map the Pacbio data to the aseembly genome by minimap2. The IGV figure is following, So, how can i know the assembly quality or which picuture can describe the result?

[colindaven]

More information needed

• eukaryotic, or bacterial etc ?
• pacbio HiFi should be good data
• gene annotation will reveal a lot more about assembly quality
• BUSCO is another good method

[wdpang]

Thanks your anwser

It's a rearrangement yeast, i only want to visual the mapping reads if complete and continuous. I will try your advice.