Using minimap2 to evaluate 'completeness' of nanopore assembly using reads

[chocotwig]

Hi,

I have assembled a genome using nanopore long reads. No reference is available for this genome. In addition to BUSCO, I want to assess the completeness of this assembly by calculating the percentage of input nanopore reads that can be mapped to the final assembly. I am thinking of using default settings, or -x -map-ont and then filtering out reads with (gapped alignment length/length of read) greater than a threshold.

Do you have any suggestions? Your help is greatly appreciated!

Thanks