An educational guide for nanopore sequencing in the classroom
Alex N. Salazar (TU Delft - Pattern Recognition and Bioinformatics)
Franklin L. Nobrega (Kavli institute of nanoscience Delft, TU Delft - BN/Stan Brouns Lab)
Christine Anyansi (TU Delft - Pattern Recognition and Bioinformatics, Broad Institute of MIT and Harvard)
Cristian Aparicio-Maldonado (Kavli institute of nanoscience Delft, TU Delft - BN/Stan Brouns Lab)
Ana Rita Costa (Kavli institute of nanoscience Delft, TU Delft - BN/Stan Brouns Lab)
Anna C. Haagsma (TU Delft - BN/Technici en Analisten, Kavli institute of nanoscience Delft)
Anwar Hiralal (Kavli institute of nanoscience Delft, TU Delft - BN/Stan Brouns Lab)
Ahmed Mahfouz (Leiden University Medical Center, TU Delft - Pattern Recognition and Bioinformatics)
Rebecca E. McKenzie (Kavli institute of nanoscience Delft, TU Delft - BN/Stan Brouns Lab)
Teunke van Rossum (Kavli institute of nanoscience Delft, TU Delft - BN/Stan Brouns Lab)
Stan J.J. Brouns (TU Delft - BN/Stan Brouns Lab, Kavli institute of nanoscience Delft)
Thomas Abeel (Broad Institute of MIT and Harvard, TU Delft - Pattern Recognition and Bioinformatics)
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Abstract
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.
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