I think you're stuck in the biotech == people mindset.
On the bacterial side, it is fantastic for quickly sequcinging and closing genomes. Personally, I think the killer use case is field portable and real time sequencing of pathogens. I've worked with groups (.gov and private, defense and health related) that want to put minION + flongles to use in applications like early detection for bio terrorism and pathogen surveillance.
I have a colleague who is working on a portable field kit with a minION + laptop + car battery with the intent of being able to sequence and identify pathogens directly in the field, even with no electric grid.
Turns out the hardest part is the sample prep. For bioinformatics, she'll just do a simple kmer mapping against a curated database of pathogen genomes.
Sample prep, particularly if you want truly long reads, is 100% the hardest part.
Funnily, there are people out there who want to teach army/marine grunts on the front line to run minIONs. Most of the work is on making the sample prep automated and idiot proof.
Who are the customers here? The waiting list for new nanopore sequencers is quite long at the moment. Our neighboring lab has been waiting on a promethION for about a year, and only just got it because their last one bit the dust putting them on top of the list.
Nanopore/pyrosequencing technology is interesting in that the class of errors that it is most susceptible to (homopolymer inaccuracies) nearly do not exist in more traditional base-by-base sequencing.
These have proven harder to correct than simple substitution errors - this is both a fault of the bias of existing tooling, and also a difficult problem in general. Roche and other companies have had a lot of smart people working on this problem.
Increasing coverage will definitely help resolve these errors, but the coverage required may be such that it's more cost effective to use a more traditional sequencer.
A homopolymer is when you have stretches of the same nucleotide, and the error is miscounting the number of them. e.g: GAAAC could be called as "GAAC" or "GAAAAC" or even "GAAAAAAAC".
What? Have you ever looked at a sanger trace with homopolymer stretches? Depending on how blotchy it is, After about 7 you might not really be sure, and it definitely gets the n wrong occasionally even with nicely resolved peaks.
I'm not defending nanopores here, frankly I'm not convinced about them yet.
Only somewhat, because the errors are systematic, and not random. Using the R9 pore flowcells, I've basically given up on getting correct consensus sequences even for influenza genomes (without manual correction, which is too labour intensive). Perhaps the new R10 pore, much better at homopolymers, will solve the problem.
there are 2 main use cases now in precision medicine: rare disease and cancer. for both you need high precision reads, which nanopore doesn't provide.