They currently specialize in different things. The larger Illumina instruments have a huge up-front cost (~$1M), tremendous throughput, low cost per base, short reads, <1% base error, and significant latency between starting sample prep and getting results back. Nanopore sequencing has trivial up-front costs, same-day results, orders of magnitude higher cost per base, >10% non-independent error rate and very long reads.

ONT will be much more useful for assembling reference genomes (which can then be polished with short reads), characterizing large scale structural variants, and real time applications like "what pathogen am I infected with?".

I expect us to use the long reads from ONT and PacBio to discover that structural variation is even more important and common than previously appreciated. If that's the case, you'd be silly to use the Illumina technology for anything more complex than population genetics, and this will probably trickle into many parts of the market as the medically-relevant parts of the field realize what the basic science is demonstrating.

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.

>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.

The simple explanation is that they are different products that only overlap to a limited degree.

If you're doing a standard RNA-seq experiment, short 100bp to 200bp Illumina reads are just dandy for what you need. Most of the time, at least; you could, for example, be interested in different splice variants for a gene family; in that case longer continuous reads are valuable. But then it's no longer a standard RNA-seq.

PacBio and pore-type sequencing is most valuable for polishing reference genome assemblies. For instance, this is a huge issue for crop plants because they have huge, repetitive genomes and are often polyploid. So there's a lot of interest in creating high quality assemblies not just for e.g. corn, but the major research inbreds (B73, Mo17, etc.) as well as private breeding lines. Some of the most valuable crop QTLs (R genes, microRNAs, transposon fragments, etc.) are just 'junk' sequence that plays a regulatory or defense role, so it's super important.

In general, the Illumina data is very high quality and very inexpensive, and works beautifully provided you have a high-quality assembly to work with, and what you're interested in isn't very repetitive. It has many good applications, so I don't see much risk at this point.

If, at some point, longer reads can be done with high fidelity and with similar cost, then there would be an issue. I don't think that's going to happen anytime soon, but I'm sure Illumina is looking at that long-term.

PacBio and ONT are far from upstarts, they have both already invested millions and millions into their respective technologies. Pacific Biosciences has a Market Cap of 532.88M Oxford Nanopore is at least as big.