Nanopore Sequencing

This lesson will introduce the Oxford Nanopore Technologies (ONT) sequencing platform, and will work through the process of generating data using an ONT sequencing device (e.g., Flongle, MinION, GridION, PromethION), moving that data to a separate compute system, then running through a typical workflow (e.g., basecalling, quality assessment, read alignment, variant calling).

Prerequisites

All pre-requisites are taken care of if you are using this lesson at the Otago Bioinformatics Spring School 2023.

Schedule

	Setup	Download files required for the lesson
00:00	1. Nanopore-based sequencing: introduction	What is nanopore-based sequencing?
00:35	2. Data Transfer	How do I get data to and from NeSI?
00:45	3. Nanopore - Basecalling	How do you perform offline (i.e., non-live) basecalling for ONT data?
01:45	4. Nanopore: quality assessment	How can I perform quality assessment of ONT data?
02:30	5. Nanopore - Variant Calling	How can I use nanopore data for variant calling?
03:30	6. Nanopore - Adaptive Sampling	How can nanopore be used for sequencing only what I want?
04:45	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.