Oxford Nanopore Technologies plc Developed a portable protein nanopore sequencing USB device to identify aspects of species and i’m curious if anyone bought it and used it and how accurate it is to identify species
I find it good, though it won’t spit out IUPAC codes so occasionally you need to open up the fastq file and double-check a sequence. It will, occasionally, spit out a chimeric sequence too so you need to watch out for it.
You still need a reference database to compare the sequences to, and there’s definitely room for user error when you’re setting up to do a run.
EDIT: Full disclosure, I’m not the sequencer in our group, I just validate.
so it does somewhat good is what i’m getting from this, like i can identify most insects and plants and such from around me??
Have you done any sequencing before?
nope but i need to learn for my goal of photographing every single species on the planet
I would probably start by finding a class on using Nanopore and going from there. It isn’t as easy as ‘stick sample in and it spits out the answer.’ You need to know what gene region serves as a barcode for the organism that you’re trying to identify - you need to have the primers for that gene region, do all the steps of DNA extraction, PCR amplification, etc, then even once you have your sequence you need to verify that it is a good sequence and compare it to the databases currently available for reference - and when comparing, you generally need to research what you’re looking at.
Mind, I have a fairly base level of knowledge about the process, most of my focus is on the data analysis portion of it.
The data analysis can get tricky; some species are well-established and have many reference sequences or type sequences available, other species still haven’t been barcoded so there’s little to reference what you get against. We’re still kind of in the infancy of high-throughput sequencing and a lot of continuing work is going to be needed to be done on the available reference databases.
So tl;dr… yes it would work for IDing species but you still would need to do validation steps once it does spit out a sequence. Also go take a class if you’re interested in it.
EDIT: also keep in mind that nanopore isn’t really cost effective unless you’re doing a LOT of specimans at once. I want to say we had close to 700 samples in our last run - if you’re only looking to doing a couple at a time, sending specimans off for sanger sequencing is probably more cost effective
EDIT2: https://mycota.com/product/dna-barcoding-with-ont-minion-course/ here is an upcoming course, if you’re interested. Mycota focuses on fungal DNA barcoding but I’m sure the techniques would be applicable to other taxa.