I dont think you can call pacbio up and coming at this point, but nanopore certainly.
And those error rate examples are way way too high - illumina is closer to Q30, which is a 1/1000 error rate[0]. 15% would result in an unusable sequence.
The sequencer may report a quality score of 30, but that doesn't guarantee that the error rate when you align to the genome will actually be 1/1000. Still, you're right that good quality Illumina data can do significantly better than 1% error rate. You can't always get "good quality" data, but I imagine that the researchers on this project probably could, given the well-controlled experimental setup.
And yes, a 15% error rate does result in a sequence that is unusable for the purposes of actually knowing the sequence. But a bunch of really long reads with 15% error can still be used to resolve the large-scale structure of a sequence, and then the lower-error-rate Illumina reads can be aligned onto this large-scale scaffold in order to resolve the actual sequence. At least, this is my understanding of how these technologies are typically used together, and given the mention of PacBio, nanopore, and Illumina, that seems to be what was done in this case.
Yes the higher error ones are used for alignment- and even then too high an error rate in a very repetitive region (especially depending on the error type - misreads vs skipped bases etc) make it too challenging to build a scaffold to align your illumina reads.
As of 2018 error rate for alignments with nanopore was around 3-6 percent
And those error rate examples are way way too high - illumina is closer to Q30, which is a 1/1000 error rate[0]. 15% would result in an unusable sequence.
https://emea.illumina.com/science/technology/next-generation...