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This isn’t the case anymore. Pathogen surveillance labs use Nanopore for single-base resolution variant calls to determine antibiotic susceptibility and to “fingerprint” against known and previously sequences isolates.

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Could you share some links on this? I’ve heard talks on using Nanopore for pathogen surveillance, but they were mostly about the ability to spit out reads once you knew what they were. Also, I sit (depending on restriction level) next to a nanopore lab, and they’re pretty consistent about nanopore not being good for single base resolution.

Maybe this could be a case with a lot of amplification, so you have many squiggles to infer a consensus from?

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