What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?
My recollection of a conversation I had with Justin O'Grady is that it's about 99% host DNA for unfiltered samples. There are a few ways to reduce that portion prior to sequencing; he has written a paper that mentions a saponin-based host depletion method that is quite effective:
https://doi.org/10.1038/s41587-019-0156-5