Re:Sequencing your DNA with a USB dongle and open source code
by Ovah on Wednesday February 03, 2021 @11:59AM
(#26015743)
Thank you for the practical insight. I suspected that NanoPores are not just yet geared towards hobbyists. I happen to have some bioinformatics knowhow so it's mainly a matter of hardware for me. As both you, u/bioinformatics and u/searine mention it is the overhead cost of flow cells etc that worries me from a hobbyist point of view.
Re:Sequencing your DNA with a USB dongle and open source code
by danpalmer on Thursday February 04, 2021 @08:34AM
(#26025157)
Yep the flow cells are expensive, but more generally saying the hardware costs $1000 is probably more of a technicality – almost all sales are bigger contracts, with training, support, flow cells, hardware, included.
Also that's great you have some bioinformatics experience, but are you sure it will apply here? I'm very unknowledgeable about this so forgive me if I'm wrong, but I believe that traditional machines do short-reads, whereas Nanopore does long-reads, which I believe invalidates many techniques for reconstructing the data, the tools, etc. This might not be something you have to be concerned about depending on the level you're working at, I don't know (maybe this is all "solved" by the time you're doing analysis?).
Re:Sequencing your DNA with a USB dongle and open source code
by Ovah on Thursday February 04, 2021 @01:19PM
(#26028182)
I think theoretical/practical background will allow me to figure stuff out as I go with relative ease. Often times in bioinformatics there are useful vignettes a Google search away. But you are right that specialized tools and libraries which I haven't used before are likely needed. At least for me the main bottleneck will be proper space for processing and the aspect of (reusable) hardware to keep costs down costs. While NanoPores appear to have hidden costs it still seems to be way cheaper than other methods if I want to have my own sequencing rig.
I don't know the answers to all your questions, but I do know that the emphasis is on research, not consumer (or hobbyist) use. I believe the devices are ~free, but each run requires using a consumable part that has to be either disposed of or returned for refurbishment, and I believe these are hundreds of dollars each.
The big advancement is the size and cost of the devices, the fact that a lab can have one on every desk rather than a communal machine that you have to queue your samples up for, or a device you can transport in field kit.
They do have cloud services that do much of the processing for you, but I suspect you'd want to be able to manipulate the data so you'd need your own data processing tools locally. It's not going to give you a 23andMe style report, it's more likely to say "yep, that's a human" vs "you're ecoli". I believe they do have training for how to do this data analysis, but I suspect this is targeted at customers on large contracts.