Richard Tillett
NV INBRE Bioinformatics
Nevada Center for Bioinformatics
ca. October 2018
Oxford Nanopore Technologies (ONT) sells a portable, real-time DNA sequencer, MinION, that is radically compact, plugs into your PC via USB 3.0, and is purportedly cheap. Is it cheap enough to use in a classroom setting as a credible sequencing device? This report doesn't attempt to speak much about the credibility of the deivce. Suffice to say, I wouldn't offer it for consideration if I thought it lacked merit. It isn't high-throughput enough to do dozens of quantitative RNA-seq samples like an Illumina is, but if you want rapid sequencing or sequencing of very long molecules, the device shines. I hope the info provided helps in cost determination.
From the MinION product page, (emphasis added):
The MinION is commercially available, simply by paying a starter-pack fee of $1,000. The MinION starter pack includes materials you need to run initial sequencing experiments, including a MinION device, flow cells and kits, as well as membership of the Nanopore Community.
Here's what comes in that $1000 starter pack. For the new customer $1000 basic package, you'd get:
| Basic Starter Pack | $1,000.00 |
|---|---|
| Flow Cell Wash Kit | 1 |
| MinION Sequencing Device | 1 |
| Starter Pack Flow Cell (R9.4) | 2 |
| Control Expansion | 1 |
| Library prep kits | 1 |
| "Enhanced support" | no |
So, you get one sequencing device (all of the MinION's electronics and structure, basically), and two of its microfluidics/nanopore guts (the R9.4 flow cells). Those flow cells are the main consumable of a sequencing run. They contain the nanopore-embedded membranes and electrode sensors that are the sequencing mechanism of this device. They do have a limited shelf life (proteins, after all), but can be safely re-used in some circumstances (see the included wash kit). And you get two of them.
That pack also nets you one library prep kit, of which there are possibly 9 to choose from, depending on the specifics of the sequencing experiment and strategy. From one view are three main flavors of kit
Or you might view the kits from whether they are "Rapid sequencing" or "Ligation Sequencing." Neither choice requires PCR, so long as you have 400 ng or 1 µg DNA, respectively. And since the nanopores have the ability to do extremely long read lengths, the PCR yes/no question is less niche and worth considering for many types of experiments, as PCR amplification protocols/kits generally produce fragments smaller than the extreme lengths ONT can generate (30 kba is not rare, they claim to have gotten as high as 2 Mba).
Any hidden costs? + Lab/IT requirements
As with the choice of kit, the exact experimental design will dictate at least one cost I don't think is included/reflected in the $1000 promo kit -- your DNA/RNA extraction kit. ONT doesn't exactly sell their own, and I think their system is compatible with plenty of the kits every mol bio lab uses, but I haven't nailed down recommendations for "best", or "ok, but change your elution buffer to ___", or "generally avoid xxx".
One other hidden cost, I think, is barcodes. If you will be multiplexing samples, you will have to buy a separate barcoding or barcoding-compatible kit.
The nanopore community site has a page listing the IT requirements (basically any recent Mac or Windows computer with a USB 3.0 plug), and the lab equipment/consumables associated with the various preps, all here https://nanoporetech.com/community/lab-it-requirements.
Flowcells start at $900, and have 512 nanopore channels, or possibly >800. Their product info makes a few different claims. You need to open the packaging, rehydrate, and do some QC on flowcells within 10 days of delivery. Need to use within 8 weeks for warranty.
Individual library prep kits range from $450-$700. There are a lot of options, but if you're specifically interested in the ultra-long read lengths of ONT, you only have to think about the no-PCR kits, and whether/how to barcode+multiplex. Shelf-life claimed to be 90 days.
They have another "starter pack" that's almost 5x as expensive, comes with 1 more kit, and 2 more flow cells. I'm not sure if it's a great value, unless you really want 3 months of enhanced support.
| Enhanced | $4909.00 |
|---|---|
| Flow Cell Wash Kit | 1 |
| MinION Sequencing Device | 1 |
| Starter Pack Flow Cell (R9.4) | 4 |
| Control Expansion | 1 |
| Library prep kits | 2 |
| "Enhanced support" | yes, 3 months |