There is not a YES / NO or single answer for your question. The answer can be in the form - Yes, but...

Oxford nanopore has several advantages and limitations too. Sure it can be used for your purpose but you can compare it with all pros and cons of other sequencing technologies before opting for one. It is cheaper but we also need to consider the cost involved in the sample library prep. May be illumina can offer integration of higher number of samples (by use of custom adapter+barcode) and the overall cost will be less.

But I have some question in your question, before I can specifically answer your question.

• What is 20 bp thing? I did not understand it? Is it the region you are interested in?
• And if you just want to quantify why is qPCR not an option? I guess qPCR quantification is better than sequencing quantification.
• Again, clones are easier and cheaper to sequence on sanger sequencer. And confirming knockouts and knockins can be also done on PCRs too.

Hi Bilsland!

I’ve MinION in my lab and have personally used it in some experiments too.

From my experience with it and a few other sequencers that I’ve personally used (IonTorrent GS S5, PGM, Illumina MiSeq and 454), I can tell you that it’s error rates and learning curves are both higher.

If you wish to resolve very minor differences in certain barcodes, you might be in a fix with the MinION/ Flongle instruments. There are new flow cells coming up which promise a better efficiency but that’s something in the future.

MinION does have many advantages but decide if you wish to take this gamble.

Hope it helps.

Feel free to discuss your use case if you want a more precise answer.

Happy ‘sciencing’!