An educational guide for nanopore sequencing in the classroom

Abstract: Genomes contain all the information required for an organism to function. Understanding the genome sequence is often the key to answer important biological questions. For example, the sequences of human genomes are used for diagnosis of genetic disorders or for the development of personalized treatments, while the sequences of microbes may inform about their mechanisms of infection and guide the development of novel drugs. Today, our capacity to generate genome sequencing data is tremendous. However, our capacity to process this information is insufficient. This is partially due to limitations of current methods for data analysis but is mostly caused by lack of training for most biologists to leverage high-throughput sequencing data and use their full potential. It is urgent that we train the new generations of biologists to become computationally aware and able to keep pace with technological developments in the field. In this manuscript, we illustrate our efforts in adopting an integrated teaching model that bridges experimental and bioinformatics works. Our course integrates data generation in the lab with bioinformatics work to illustrate the interlinking of lab practices and downstream effects. In our demonstration course, we used nanopore sequencing to train nanobiology students, but the model is easily customizable to suit students of different educational backgrounds or alternative technologies. The tools we provide help not only science educators but also biologists to address many relevant questions in biology.

Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, et al. An educational guide for nanopore sequencing in the classroom. PLoS Computational Biology, 26(1): 2020.
@article { bib:2020_ploscompbio_edu,
author = { Alex N. Salazar and Franklin L. Nobrega and Christine Anyansi and Cristian Aparicio-Maldonado and Ana Rita Costa and Anna C. Haagsma and Anwar Hiralal and Ahmed Mahfouz and Rebecca E. McKenzie and Teunke van Rossum and Stan J. J. Brouns and Thomas Abeel },
title = { An educational guide for nanopore sequencing in the classroom },
journal = { PLoS Computational Biology },
volume = { 26 },
number = { 1 },
year = { 2020 },
doi = { doi.org/10.1371/journal.pcbi.1007314 },
}