Oxford Nanopore sequencing in a research-based undergraduate course

Background: Nanopore sequencing is a third generation genomic sequencing method that offers real time sequencing of DNA samples. Nanopore sequencing is an excellent tool for teaching because it involves cutting-edge sequencing methods and also helps students to develop a research mindset, where students can learn to identify and resolve problems that arise during an experiment.

Results: We, as a group of undergraduate biology students, were able to use nanopore sequencing to analyze a sample of pupfish DNA. We were able to accomplish this without computer science backgrounds and only some basic DNA extraction training. Although there were issues, such as inconsistent results across runs, we found it useful as a research learning experience and an application of the skills we learned.

Conclusions: As students, it was exciting to be able to experience this technology first hand and apply what we learned in the classroom. Nanopore sequencing holds potential for DNA sequencing of large fragments in real time. It allows students to be acquainted with novel technologies and the theories behind them. However, as with all new techniques, it does not have the same established support, and when students run into difficulties while using nanopore sequencing, it is often difficult to identify what went wrong.