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This would be me more applicable to looking for variants of a known gene. For example, measuring mutation rates within known covid-positive samples.

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Nanopore isn’t great for looking at generic mutation rates (many will be single nucleotide polymorphisms) due to the high error rate. It’s much better at looking for splicing patterns and epigenetic modifications. Splicing patterns could conceivably change due to mutation, but that’d be a pretty dramatic mutation.

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.

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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