Thank you. The upfront cost of the sequencer sure makes it tempting at first sight.

My desired hobbyist use case is to key out plants, lichens and mushrooms that I find in the field. I have the bioinformatics knowhow just need the hardware. 3-4h seems lika a long time for a genome that is <30k nucleotides long. Mushrooms on average seem to have almost as many genes as coronaviruses has nucleotides. I guess partial sequences (and thus reduced comp time?) might do the trick but it's probably hard to target those partial reference sequences with a long-read method like NanoPore.

If you repeat the process many times will it reduce that error rate, or are the errors non-independent?

Unfortunately, with nanopore the errors are biased so you tend to get errors in the same places. All sequencing techniques also have error rates but some are unbiased so running a single sample through (which will usually have many, many copies of any sequence) will average out to a good read of the sequence.

Some good info on next-gen sequencing techniques: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841808/

Still, some of the errors can be compensated for with more coverage. So if you can manage 20-30X you're left with the homopolymer problem (nanopores can't tell how long a stretch of the same repeated nucleotide is, because you can't control how long the sensed kmer stays in the pore), but lots of other types can be improved quite a lot.

Last time I looked into Nanopore the cost wasn't that much better where you'd even consider this experiment.

On the other hand, when doing a genome assembly, the Nanopore reads are good for a draft sequence and then the Illumina reads can be used to polish the sequence.

Is the error rate per base pair?