For use case of hybrid assembly, we find that when you need not only an accurate but also contiguous denovo assembly. Hybrid assembly works really great because you're combining the best of both worlds, accurate short illumina sequencing and to span the gaps or ambiguous paths across contigs; use the Nanopore longer reads. This is important for use cases such as genomic surveillance of novel changes (e.g., synthetic engineering or horizontal or foreign gene transfer) - as you can't rely on a reference genome but need to detect a small change in the genome in an denovo fashion.

For use case of iterative synthetic biology design, we find that Illumina short reads don't cut it when you're doing a high throughput screen sequencing of a pool of say synthetic genes where they have similar barcodes, promoters or gene sequences (you're screening for which family of enzyme would work best, so you end up with sometime very homologous sequences). Because Illumina's 100-250bp doesn't span the entirety of a sequence and having a pool of very similar sequence makes the demultiplexing very tricky. We used Nanopore and the results were mixed given the high error rate of MinION.

Just sharing b/c it's been interesting to hear other people's application of Nanopore MinION!

> Anyone have an idea of a market or research project where this thing is a first-choice tool?

Plants. They often have huge genomes with sections that are hard to sequence with traditional methods with shorter read lengths.

The part I was really interested in was why portability matters, instead of just having a bench-top Nanopore. I think the idea is that it will be more hobbyist friendly, would be fun to sequence random stuff while hiking. My concern is that the market for these devices isn’t actually that large, as any place doing meaningful analytics is probably going to want a bench top unit.

Looking at the prices, now, though I think $1,000 for the minION is about what I’d be willing to pay for that vs a $50,000 benchtop unit. The fact that it does RNA too is huge, as that has a lot of benefits to doing it as close to site of harvest.

It's possible to learn from guidebooks, but I often find the descriptions a bit hard to interpret.

With plasmids, you can also train custom models to get better alignment results.

It’s insane that nobody else I know of is doing this, since it actually works quite well!

In my experience, Sanger is less accurate than Nanopore, especially since you’re getting 1x coverage per read, and in order to reliably get good coverage of sequence you need a primer every 600 base pairs.

Consensus reads on Nanopore aren’t that bad, and you can automate them way better than Sanger. I haven’t found any issue using them - IMO the “it isn’t accurate” stuff isn’t very accurate.

Also, base pair resolution is bad on Nanopores primarily at homopolyer stretches. Guess what you can’t synthesize in the first place?

(Edit: I’ve done Sanger sequencing on about 3,000 plasmids at once before for high throughput cloning, and that SUCKED.)