An educational guide for nanopore sequencing in the classroom

An educational guide for nanopore sequencing in the classroom

Salazar, A.N. (TU Delft Pattern Recognition and Bioinformatics)
Luzia de Nobrega, F. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
Anyansi, C.A. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard)
Aparicio Maldonado, C. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
Martins Costa, A.R. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
van Eijkeren-Haagsma, A.C. (TU Delft BN/Technici en Analisten; Kavli institute of nanoscience Delft)
Hiralal, A.A. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
Mahfouz, A.M.E.T.A. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center)
McKenzie, R. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
van Rossum, T. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
Brouns, S.J.J. (TU Delft BN/Stan Brouns Lab; Kavli institute of nanoscience Delft)
Abeel, T.E.P.M.F. (TU Delft Pattern Recognition and Bioinformatics; Broad Institute of MIT and Harvard)

2020

The last decade has witnessed a remarkable increase in our ability to measure genetic information. Advancements of sequencing technologies are challenging the existing methods of data storage and analysis. While methods to cope with the data deluge are progressing, many biologists have lagged behind due to the fast pace of computational advancements and tools available to address their scientific questions. Future generations of biologists must be more computationally aware and capable. This means they should be trained to give them the computational skills to keep pace with technological developments. Here, we propose a model that bridges experimental and bioinformatics concepts using the Oxford Nanopore Technologies (ONT) sequencing platform. We provide both a guide to begin to empower the new generation of educators, scientists, and students in performing long-read assembly of bacterial and bacteriophage genomes and a standalone virtual machine containing all the required software and learning materials for the course.

http://resolver.tudelft.nl/uuid:bf190e26-4afd-4f77-9e96-a922207ecdd5

https://doi.org/10.1371/journal.pcbi.1007314

1553-734X

PLoS Computational Biology (Print), 16 (1), e1007314

Institutional Repository

journal article

© 2020 A.N. Salazar, F. Luzia de Nobrega, C.A. Anyansi, C. Aparicio Maldonado, A.R. Martins Costa, A.C. van Eijkeren-Haagsma, A.A. Hiralal, A.M.E.T.A. Mahfouz, R. McKenzie, T. van Rossum, S.J.J. Brouns, T.E.P.M.F. Abeel