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Mastering Whole genome Sequencing and Metagenomics using Oxford Nanopore Long Read Sequencing. Bench-lab training


Technical University of Denmark


General course objectives:
In the rapidly evolving field of genomics and disease diagnostics using sequencing, Oxford Nanopore Technologies (ONT) stands out as a cutting-edge technology enabling real-time, long-read sequencing, with portable devices when sufficient equipment are available. This course is designed to equip PhD students and professionals with in-depth knowledge and hands-on experience in ONT usage. It's a gateway to mastering a technology that's taking over genomic research, diagnostics, and personalized medicine. We will start with a brief introduction into ONT technology and devices, with the goal of covering biological samples to sequencing data workflows for: whole genome sequencing (WGS) from bacteria, metagenomics from faeces and 16S rRNA sequencing from faeces as preliminary examples. This course will cover the wet lab preparation of HMW DNA extractions, and libraries from genomic DNA, with a focus on the critical steps and potential pitfalls and understanding what constitutes a ‘good’ sample for purpose of best results using the technology. Other library preparation methods can be covered upon advanced requests. The training also includes an overview of the sequencing platform and software: GridION, MinION devices, in addition to P2 Solo upon special request. Brief knowledge of ONT is desirable but not essential. Capacity: 15-20 participants. While this is a stand-alone course, it is followed by an accompanying bioinformatics and data analysis course, which ties both this bench lab course with a dry lab part (the dry lab and analysis course is course number: 23841).

Learning objectives:
A student who has met the objectives of the course will be able to:
  • Recognize the fundamental concepts and workflows of Oxford Nanopore Sequencing as changes in electrical current to represent DNA sequences.
  • Identify the components and functionalities of ONT devices.
  • Explain the principles of HMW DNA extraction and be able to perform it.
  • Link the quality of HMW DNA to Long Read Sequencing quality using ONT.
  • Perform sample preparation, DNA extraction and sequencing runs using ONT.
  • Apply ONT techniques to real-world genomic research problems and on-site sequencing (in the field).
  • Analyze and troubleshoot sequencing data to assess quality and accuracy.
  • Interpret the basic data analyses from the sequencing runs.
  • Design and conduct a mini-research project using ONT, integrating theoretical knowledge with practical skills.
  • Implement ONT into your own research questions.

Contents:
Course Structure: The course will include very few and short theory sessions to start the day and introduce the concepts. Then followed by bench work for the remainder of the day. The course will finish with applying the learned methods and protocols to the participant own research. We encourage the participant to bring their own samples after a discussion with the course responsible. There will be reading materials (mainly protocols) to be covered by the participants before the start of the course. The course will provide 2 ECT credits to the PhD students which is evaluated through a report with pass/not pass grading (this part is only for PhD students).

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Course organizer
Saria
Place/Venue
Anker Engelunds Vej 1
City
2800 Kgs. Lyngby
Country
Denmark
Workload
2
Link
http://kurser.dtu.dk/course/23842