Ten Steps to Getting Started with Nanopore

Essential steps for getting started with Nanopore sequencing

1. Understand the Basics of Nanopore Sequencing
   • Familiarize yourself with how Nanopore sequencing works, its capabilities, and its limitations.
     • Review this book chapter: The Current State of Nanopore Sequencing 2023
     • View Nanopore's video: How to get started with nanopore sequencing and plan your experiment
     • Review advanced research Applications making use of Nanopore sequencing.
2. Assess Your Curriculum Goals
   • Define the objectives for integrating Nanopore sequencing into your classroom.
   • Determine whether you will focus on specific applications (e.g., microbial diversity, genome assembly, or barcoding) or introduce students to the general principles of sequencing.
   • Know benefits and strategies for introducing course-based research experiences.
     • Find resources for developing undergraduate course-based research experiences: Fear of the CURE: A Beginner’s Guide to Overcoming Barriers in Creating a Course-Based Undergraduate Research Experience
3. Plan and Budget for Equipment and Materials
   • Use our list of essential equipment (e.g., MinION sequencer, magnetic racks, pipettes) and reagents (e.g., DNA extraction kits, sequencing kits).
     • We recommend starting with the 16S demonstration experiment or DNA barcoding demonstration experiment to get started. Each experiment details all the needed materials.
     • Use educational discounts where available to minimize costs.
     • Check with colleagues at your institution or nearby who may be using Nanopore and can provide you with support.
4. Set Up Online Accounts and Software
   • Register for an Oxford Nanopore Technologies account.
     • Orders for Nanopore devices, library kits, reagents and accessories at the Nanopore store.
       • You will likely need to coordinate with your purchasing department to setup shipping and payment.
       • Orders can also be placed through an authorized vendor such as Avantor; check with Nanopore on additional options.
     • You will be able to purchase a starter pack to get your device.
   • Explore free platforms like Galaxy, DNA Subway, and CyVerse for bioinformatics workflows.
5. Acquire Hands-On Experience
   • Conduct trial runs of Nanopore workflows before teaching.
   • Practice key steps such as DNA extraction, library preparation, and sequencing.
   • Use mock samples or pre-prepared datasets to familiarize yourself with bioinformatics tools.
6. Develop or Adapt Teaching Materials
   • Prepare slides, handouts, and protocols tailored to your specific learning objectives.
   • Include clear instructions for students on safety, experimental techniques, and data analysis.
   • Incorporate assessments to evaluate students’ understanding and progress.
7. Engage in Protocol Optimization
   • Test protocols with your lab aides or instructional staff to identify potential bottlenecks.
   • Adjust protocols for compatibility with your class size, time constraints, and available resources.
8. Plan Your First Experiment
   • Choose a simple and achievable experiment (e.g., sequencing microbial DNA or barcoding plant species).
   • Use small-scale experiments to build student confidence and refine your approach for larger projects.
   • Layout how sequencing work will be divided between individual students, student groups, and instruction staff.
9. Leverage Community Resources
   • Join educator-focused communities like our QUBES network and Nanopore Network Slack.
   • Attend faculty mentoring networks, webinars, or in-person training sessions to exchange knowledge and strategies with peers.
10. Evaluate and Iterate
    • After your first experiments, evaluate student outcomes and overall workflow.
    • Gather feedback from students and instructional staff to refine future experiments and lesson plans.
    • Document your experience to build a robust and repeatable curriculum.