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The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis. In the near future, anyway, I would expect to see inaccurate PacBio/Nanopore long reads being used as scaffolds for accurate Illumina short reads (in fact, this is already happening). Illumina won’t be going anywhere any time soon.

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>The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis.

This is true, but only for Insertions/Deletions. The substitution error rate is comparable to Hi-Seq.

So it's good for resequencing but without a reference or decent scaffolds, you're in the dark.

I've only sequenced a few samples on a MinION. The dominant error seemed to be miscounting the length of a homopolymer stretch (e.g. CCC->CCCCC) but the substitution error rate was also clearly worse than Illumina. I've gotten used to less than 0.1% error from DNA sequencing on a HiSeq 2500. My guess is that the MinION data had 1-3% substitution errors.

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