Distinguishing closely-related strains in Nanopore metagenomics data

Question

[megoo]

Hi - we have a bunch of high-diversity environmental metagenomics samples. I am trying to figure out whether our samples that are positive for a pathogen of interest are representing a true hit, or if the hit just represents contamination from the spike-in standard.

So to clarify, I want (some degree of) strain-level resolution for long-read metagenomics data - and I can't seem to find a tool designed for long read data that doesn't rely on MAG assembly.

Currently I am thinking I will take my species-binned reads and try to blast against a database of marker/typing genes for the species.

I am very confident there is a better way of doing this, and would appreciate any advice. Thanks in advance!