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Getting Started with Nanopore Sequencing

Why Nanopore sequencing is promising for education

For decades, education leaders have emphasized the need to expand and strengthen the STEM workforce. Among the many strategies to achieve this goal, providing students with authentic research experiences has proven to be the most effective. Research participation significantly increases the likelihood that students will persist in and complete STEM degrees. Yet, one major challenge remains: ensuring that all STEM students, regardless of their institution or background, have access to meaningful research opportunities.

Nanopore DNA sequencing is uniquely positioned to address this challenge. This portable, low-cost technology has democratized access to DNA sequencing, placing powerful research tools within reach of pre-college and college classrooms. The same technology used by top researchers can now empower students to investigate their own scientific questions, fostering deeper engagement and understanding.

Integrating DNA sequencing into STEM curricula unlocks numerous benefits:

  • Active Learning: Students gain hands-on experience with cutting-edge technology, transforming abstract concepts into tangible discoveries.
  • Skill Development: From molecular biology to data science, students build multidisciplinary skills critical for the modern STEM workforce.
  • Ethical Research Practices: Teaching responsible research conduct equips students to navigate complex challenges in the scientific and societal spheres.

National networks of bioscience educators and industry professionals have demonstrated the transformative potential of course-based research experiences. Scalable and engaging, DNA sequencing-based research experiences can reach large numbers of students, providing an equitable pathway into science. With coordinated efforts, we can bring these opportunities to classrooms across the country, ensuring that all students have a chance to engage meaningfully with science.

Accessible DNA sequencing is more than just a tool for examining the blueprint of life—it’s a roadmap for advancing STEM education and cultivating the next generation of scientists.

What is Oxford Nanopore sequencing?

Oxford Nanopore sequencing is an innovative technology that allows scientists and students to sequence DNA by passing molecules through tiny nanopores embedded in a membrane. As the nucleic acids move through the nanopores, they create electrical disruptions, which are analyzed in real-time to determine the sequence. This method enables quick, portable, and cost-effective sequencing—ideal for educational settings.

For a beginner-friendly overview, watch the short introductory video How nanopore sequencing works on the Oxford Nanopore Technologies YouTube channel. It explains the basic principles of the technology.

How Nanopore sequencing works

Key features of Oxford Nanopore sequencing include:

  • Low Cost: Oxford Nanopore devices have significantly lower startup costs compared to traditional platforms, making advanced DNA sequencing more accessible.
  • Student-friendly: With a little training, a high school or undergraduate can do every step of most sequencing workflows. With some experience, the entire Nanopore sequencing workflow is something students can reliably operate.
  • Portability: Devices like the MinION are small enough to fit in your pocket, making them accessible for classroom use. Sequencing can be done in the classroom, rather sent off to some remote institution. This builds local capacity and turns institutions that may not have previously participated into potential genome sequencing centers.
  • Real-Time Data: With real-time data streaming, educators can engage students in experiments where results are visible immediately, enhancing the learning experience.
  • Long Reads: The technology excels at sequencing long DNA fragments, providing insights into complex genomic regions that are difficult to analyze with traditional methods.

Oxford Nanopore sequencing has been used in groundbreaking projects, from sequencing genomes in space to tracking viral outbreaks like SARS-CoV-2. Its versatility and affordability make it a powerful tool for transforming biology education, enabling students to engage with modern research techniques and develop essential skills in molecular biology and data science.

How accurate is Nanopore sequencing?

>99% accuracy and improving

In the early development of the technology more than a decade ago, Nanopore sequencing had significant issues with sequence quality. That is no longer the case. The quality of Nanopore data is not only suited for the classroom, but in real research application — for example in the completion of the human genome. In addition to the chemistry improvements that have helped, error correction methods have further improved the quality of the data you can generate.

Oxford Nanopore makes these claims about the accuracy of it's platform. We also recommend you examine the latest peer-reviewed research. Here are some helpful papers:

  • Stevens, B.M., Creed, T.B., Reardon, C.L. et al. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Sci Rep 13, 9323 (2023). https://doi.org/10.1038/s41598-023-36101-8
  • Cuber, P., Chooneea, D., Geeves, C., Salatino, S., Creedy, T. J., Griffin, C., Sivess, L., Barnes, I., Price, B., Misra, R. (2023). Comparing the accuracy and efficiency of third generation sequencing technologies, Oxford Nanopore Technologies, and Pacific Biosciences, for DNA barcode sequencing applications. Ecological Genetics and Genomics, 28, 100181. ISSN 2405-9854. https://doi.org/10.1016/j.egg.2023.100181.
  • Zhang, T., Li, H., Jiang, M., Hou, H., Gao, Y., Li, Y., Wang, F., Wang, J., Peng, K., Liu, Y.-X. (2024). Nanopore sequencing: flourishing in its teenage years. Journal of Genetics and Genomics, 51(12), 1361–1374. ISSN 1673-8527. https://doi.org/10.1016/j.jgg.2024.09.007.

What does a Nanopore sequencing workflow look like?

Example DNA Barcoding Workflow

We routinely do complete experiments—sample collection to data analysis—in one day. Several factors impact how much time is needed, but this example is fairly representative:

PCR amplicon sequence (as presented on Oxford Nanopore protocol page).

Basic Steps

  • PCR: 1-3 hours (there are PCR-free methods such as genome sequencing)
  • PCR clean up (and, we'd recommend quantification): 60 min
  • Library prep (adapters added and sample prepared): 45-60 min
  • Sequencing: Useful data in 30-60 min, longer runs for additional data
  • Data analysis: Realtime analysis can generate results in minutes, and many datasets (e.g. DNA barcoding) can be analyzed in under 20 minutes. Many analyses don't require any coding or complex bioinformatics skills.

Am I ready to bring Nanopore sequencing into my classroom?

To determine your readiness to integrate Nanopore sequencing into your classroom, consider the following self-assessment. Rate yourself for each consideration on a scale of 1–3:

  • 1: I’m just starting out or have limited experience/resources in this area.
  • 2: I have some experience/resources but may need additional preparation or support.
  • 3: I’m confident, well-equipped, or fully prepared in this area.

Keeping score

Use the checkboxes to keep track of your self-assessment scores.

1. Technical readiness

  • Access to Equipment: Do you have the necessary devices (e.g., MinION sequencer, Flongles), molecular biology reagents (e.g., DNA extraction equipment, micropipettes, PCR machine), a laptop, and other essential peripherals?

    • 1 - I don’t yet have access to these tools.
    • 2 - I have some access but may need additional equipment.
    • 3 - I have full access to all required tools.

  • Laboratory Facilities: Is your lab space equipped for basic molecular biology work (e.g., pipettes, centrifuges, PCR)?

    • 1 - My lab is not set up for molecular biology or I don't have lab space.
    • 2 - My lab has some resources but might need upgrades.
    • 3 - My lab is fully equipped and ready.

2. Training and expertise

  • Familiarity with DNA Sequencing: Do you have foundational knowledge of DNA sequencing techniques?

    • 1 - I’m new to DNA sequencing.
    • 2 - I have some understanding but may need additional training.
    • 3 - I’m confident in my understanding of DNA sequencing.

  • Bioinformatics Knowledge: Do you or your students have basic skills for analyzing sequencing data?

    • 1 - I have no bioinformatics experience.
    • 2 - I have some familiarity but need further support.
    • 3 - I have sufficient knowledge to analyze sequencing data.

3. Budget and resources

  • Cost of Reagents: Do you have funding for consumables like sequencing kits and flow cells?
    • 1 - I don’t have a budget for reagents yet.
    • 2 - I have some funding but may need to secure more.
    • 3 - I have a reliable budget for necessary materials.

4. Curriculum alignment

  • Course Goals: Does integrating Nanopore align with your course’s learning objectives?

    • 1 - I’m unsure how this fits into my course.
    • 2 - I see potential alignment but need to refine objectives.
    • 3 - Nanopore integration fits perfectly with my objectives.

  • Time Commitment: Can your curriculum accommodate the time for sequencing experiments and data analysis?

    • 1 - My schedule is too tight for this addition.
    • 2 - I can make room but may need careful planning.
    • 3 - My schedule can fully support this integration.

5. Student readiness

  • Skill Level: Are your students prepared to engage with molecular biology and data analysis concepts?

    • 1 - Students have minimal exposure to these concepts.
    • 2 - Students have some familiarity but need more preparation.
    • 3 - Students are well-prepared for these activities.

  • Engagement: Are your students likely to find the experiments and research questions motivating?

    • 1 - Students may find this unfamiliar or challenging.
    • 2 - Some students might be engaged; others need motivation.
    • 3 - Students will be highly motivated by these activities.

6. Community and support

  • Mentorship and Networks: Are you part of an educator community that can support you in implementing Nanopore sequencing?
    • 1 - I don’t have a network to rely on.
    • 2 - I have some connections but would benefit from more support.
    • 3 - I’m part of a strong community of educators.

7. Ethical and inclusive practices

  • Responsible Conduct of Research: Are you ready to teach ethical considerations like data handling and equity in research?

    • 1 - I’m unfamiliar with these practices.
    • 2 - I have some knowledge but need more preparation.
    • 3 - I’m confident in teaching these topics.

  • Inclusivity: Can you design lessons that connect sequencing to student- and community-relevant topics?

    • 1 - I’m unsure how to make lessons relevant.
    • 2 - I have ideas but need more resources.
    • 3 - I can confidently create relevant and engaging lessons.

What do my scores mean?

If you are mostly scoring 2 or above, you are likely ready to bring Nanopore sequencing into your classroom. Even if you rated yourself lower in some areas, don’t worry—this guide is designed to provide the support, resources, and community you need to get started and build confidence.

Remember, teaching with new technology is a learning process for both you and your students. Embrace the opportunity to grow together while exploring the exciting world of Nanopore sequencing!

Training opportunities

Training Opportunities

In addition to the resources on this site, please bookmark the faculty training page of the DNA Learning Center. We will post regular free training opportunities.

From absolute beginner to competent and confident

Embarking on the journey to integrate Nanopore sequencing into your classroom can feel daunting at first, but with the resources provided on this site, you’ll be fully supported as you progress. Whether you’re new to DNA sequencing or just unfamiliar with Nanopore technology, this site is designed to guide you step-by-step, helping you grow from your first experiment to confidently leading students through research experiences.

What this site offers

  • Getting started checklists
    These checklists will help you ensure you have the minimum equipment needed to begin, understand the time and costs involved, and plan effectively for your first experiments.

  • Demonstration experiments
    Explore classroom-friendly experiments with detailed protocols, tips, and troubleshooting advice. These experiments are great starting points, enabling you and your students to gain hands-on experience with Nanopore sequencing.

  • Bioinformatics guides
    Even if you have limited computational skills, our bioinformatics sections provide straightforward protocols to help you get set up. Step-by-step guidance ensures you can analyze sequencing data and interpret results with confidence.

  • Example datasets
    Use curated datasets to familiarize yourself with the outcomes of a typical experiment. These examples allow you to practice data analysis and understand what to expect when working with real sequencing results.

  • Teaching resources
    Discover examples of effective teaching practices and approaches. From lesson plans to strategies for engaging students, these resources will inspire you to integrate Nanopore sequencing into your curriculum in meaningful ways.

  • Community and peer support
    Connect with other educators who are also implementing Nanopore sequencing in their classrooms. Join virtual communities like the QUBES Nanopore Network and our Slack group to exchange ideas, share experiences, and troubleshoot challenges. Additionally, periodic opportunities for in-person training will allow you to build hands-on skills and grow your network.

A journey of growth

Remember, this is a journey—not a sprint. You don’t need to master everything at once. Start small, with a single experiment or activity, and build from there. Over time, you’ll develop skills in experimental techniques, data analysis, and instructional design.

As you progress, you’ll gain confidence and competence, and your students will benefit from engaging in authentic research experiences. Whether you’re teaching molecular biology, genetics, or data science, Nanopore sequencing can become a transformative tool in your classroom. Go at your own pace, and know that this site and its vibrant community are here to support you every step of the way.

Comments and discussion

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