The first DNA 'tricorder' in your pocket
phys.org
phys.org
Anyone have an idea of a market or research project where this thing is a first-choice tool?
Edit: I stand corrected, seems some people are trying to use it in front-line clinical tests with post-analysis accuracy roughly on par with Illumina machines.
> 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.)
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!
https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies
This does not seem to bode well for privacy.
The same can be said about cameras. And DNA tracks are easier to fake.
Yes, it could be used to build a database, so long as you have a good amount of DNA from the person. Honestly, governments are already doing this with Illumina runs, so no diff there really.
It immediately generates runs, and tapers off at about 12-24 hours, and using a full flow cell takes like 48. How long you run it for depends on depth of reads.
Flongle flow cells cost $99 and approximately $200 at end of day and minion flow cells cost about $1000, with minion being about 10x as good as flongle. The primary cost is definitely consumables, the capex for these devices is very low.
The weird thing in this article is that they say that "Most of the studying of DNA: aligning, analyzing, is done on large server clusters or high-end laptops." but that an iPhone app can replace that. In my experience, aligning is not computationally intensive at all.
I thought it was more like an ethereal chromatography device.
That scanning seems to work down to the molecular level, because IIRC it's often used to check for "DNA degradation/mutation/etc", which is a common enough plot point. That implies the ability to take DNA sequences.
But this is just another case of a company trying to ride the Trek-tech bandwagon. A real "tricorder", or anything close, would be a massive leap forward in technology, even if it came in the bulky TOS-style boxes.
The DNA sequencer used costs around 1000 usd, and has bluetooth and wifi connectivity.
Any chance for an Android app? Or something open so we can create it ourselves, e.g. OpenDNA?
Is DNA analysis that complicated once you have the raw data?
https://nanoporetech.com/products/minion-comparison
A new flow cell is needed for every run, pricing for them is in the "Price per flow cell" row.
The raw data is actually pretty intense to decode - it took my 4 core i7 processor (2016) about 30 hours to basecall like 3gb of data from a flongle, which normally on minion flow cells you get like 30gb. This can be greatly increased with GPUs, however.
Nanopore is very locked down, but data you can share freely.
Windows – 7, 8, 10
OSX – Sierra, High Sierra, Mojave, Catalina
Linux – Ubuntu 16.04 or 18.04