how is panacus treating Ns about panacus HOT 4 CLOSED

Panacus does not detect Ns, so it counts them as if they were resolved. A 1000 Ns in the human genome won't lead to a steep curve, even if you have 100 haplotypes. You probably won't see the effect--for comparison, the are euchromatic 82Mb in the hprc-v1.0-pggb graph that are unique, i.e., not shared by two ore more genomes. The most accurate way to treat them would be to exclude them from growth calculation, using Panacus' --exclude feature.

from panacus.

Ah, I need to take a closer look at the --exclude feature.

from panacus.

Thanks!

from panacus.

Ah, I need to take a closer look at the --exclude feature.

That, or actively include regions that you're sure about with --subset.

from panacus.