Faculty Professional Development Workshop
Summer of Nanopore 2025
Nanopore Training Workshop
Summer 2025
Thanks to funding and support from the U.S. National Science Foundation and Oxford Nanopore Technologies the Cold Spring Harbor Laboratory DNA Learning Center is once again offering a series of three-day workshops designed to help faculty bring Nanopore sequencing into their classrooms.
2025 Workshops
- May 14–16: Arecibo C3 STEM Center, Arecibo, PR
- June 2–4: Kennedy-King College, Chicago, IL
- June 9–11: Pima Community College and Arizona-Sonora Desert Museum, Tucson, AZ
- June 23–25: Forsyth Tech Community College, Winston-Salem, NC
- June 30–July 2: Dolan DNA Learning Center, Cold Spring Harbor, NY
- August 6–8: San Jacinto College, Generation Park, Houston, TX
2025 Support
Supported by grants from the U.S. National Science Foundation Advanced Technological Education Program (#1901984), and Arecibo Center for STEM Education and Research (#2321729). Equipment and supplies provided by Oxford Nanopore.
Pre-workshop preparation
Preparation for this workshop does not require extensive time. There are some things you can do in advance to fully prepare:
Background Reading
Before you arrive, you may want to familiarize yourself with Nanopore sequencing technology. Review the Start Here section of this e-book, which has useful links and videos that can familiarize you with the basics.
Join the Slack
During and after the workshop, Slack, a platform for shared chat messaging, is one tool we use to stay in touch. Join the Nanopore Educator's Slack and use the #introductions channel to introduce yourself to the community and share a little about yourself and your interest. New to Slack? We will review during the workshop.
Bring a sample
This year, we plan to four sample experiments. For the DNA Barcoding experiment, you may bring a plant sample (e.g. a leaf or flower). You will also provide a sample of cheek cells for the human mitochondrial lab. At the workshop you will collect a microbial sample for the 16S barcoding and we will provide a sample for whole-genome sequencing.
Bring a laptop
We recommend bringing a laptop that can connect to the internet. If you do not have a laptop, please email your workshop contact to see if a computer can be provided.
Prepare your questions
Please commit to sharing your questions and providing feedback. It will be useful to have a notebook or file for questions you generate before, during, and after the workshop. You will have multiple opportunities to ask these questions and provide feedback, including through a survey. We are especially interested in how resources such as this e-book can be improved to suit your needs and those of your students.
Install software (Optional)
You may wish to install the EPI2ME software (as well as Docker software; required for EPI2ME) compatible with your operating system. You may also install the MinKNOW software that is used to run the Nanopore sequencing device (you will not be required to use the MinKNOW software in the workshop, but you may want to be familiar with it.) Please see Software Installation and Management for installation instructions.
Setup a Nanopore account (Optional)
If you do not have a Nanopore account you can register here. You will need an account to access some areas of the Nanopore site, including official protocols. You will also need to setup to be able to purchase materials and have them shipped to you. Joining the "Education Beta" will enable you to access substantial discounts on Nanopore products.
Workshop agenda
This sample agenda is gives you a sense of the timing and experiments we intend to cover and is subject to adjustment.
Day One
| Time | Activity | Links | Notes |
|---|---|---|---|
| 09:00am | Workshop objectives, concepts, workflows, and intros | ||
| 09:30am | DNA extraction from plants and cheek cells (Chelex) | ||
| 10:00am | PCR of rbcL and human mitochondiral control-region PCR | ||
| 11:00am | Introductions, Nanopore and e-book tour | ||
| 12:00PM | LUNCH | ||
| 01:00pm | Agarose gel electrophoresis rbcl / mtDNA PCR | ||
| 02:00pm | Rapid library preparation of rbcl / mtDNA amplicon | ||
| 03:00pm | Sequencing of rbcl and mtDNA amplicons | ||
| 04:00pm | Analysis of DNA barcodes with DNA Subway 2.0 |
Day Two
| Time | Activity | Links | Notes |
|---|---|---|---|
| 09:00am | Review analysis of DNA barcodes and mtDNA | ||
| 11:00am | Microbial DNA extraction from swabs | 16S Protocol | |
| 12:45pm | 16S PCR | ||
| 01:00pm | LUNCH | ||
| 02:00pm | Agarose gel electrophoresis | ||
| 02:30pm | Rapid library preparation of 16S metabarcodes | ||
| 4:00pm | Genome sequencing using MinION flow cell |
Day Three
| Time | Activity | Links | Notes |
|---|---|---|---|
| 09:00am | Analysis of 16S metabarcoding and bacteria genome assembly | ||
| 10:30am | Genome assembly and annotation | ||
| 12:00pm | Group self-assessment and | ||
| 01:00pm | LUNCH, classroom implementation discussion, survey |
Learning Outcomes
Taking this workshop, we hope you walk away with the following outcomes:
Technical
- Understand the basics of how Nanopore sequencing works
- Able to narrate the “how nanopore works” video
- Explain the difference between ligation and rapid methods
- Explain how the pore “reads” DNA
- Explain what is happening in basecalling
- Understand the breath of applications (short/long reads, RNA, methylation, protein)
- Know how to prepare a sample for Nanopore sequencing
- Extract DNA and test quality
- Follow the appropriate library prep protocol
- Understand how to load and run a sequencing experiment
- Understand the differences in flow cells
- Explain the differences in flow cell loading protocols
- Be able to test a flow cell
- Be able to start an experiment using MinKNOW
- Understand the metrics output by MinKNOW
- Understand basic sequence statistics
- Recognize an acceptable vs. unacceptable sequencing run
- Recognize the outputs of Nanopore sequence data
- Know what a Fast5 and a FastQ file is
- Understand what information these files contain
- Choose downstream analyses for Nanopore data
- Know what Dorado is
- Know what QC software is (e.g., FastQC or FastP)
- Know what assembly software does
- Know what EPI2ME is
- Understand options for more custom analyses (e.g. Jupyter)
- Obtain essential hardware and install essential Nanopore software
- Know minimal computer specifications
- Know minimal laboratory equipment
- Install MinKNOW
- Install EPI2ME labs
- Access JetStream for high-powered analyses
- Access DNA Subway 2.0 (coming soon)
Pedagogical
- Be able to explain Nanopore sequencing in the context of other methods
- Explain “NGS” sequencing is and how it has evolved over the last 20 years
- Explain the price advantage for Nanopore sequencing
- Explain the value of DNA sequence for life science dicipines
- Identify potential applications of Nanopore sequencing for student projects
- See examples of how sequencing projects (DNA Barcoding 101)
- Review example papers and projects and resources for identify additional examples
- Connect with other educators and get support as you develop curricula
- Exchange contact information
- Join the Slack
Practical
- Know how to navigate the Nanopore website and place orders
- Obtain a Nanopore account and bookmark essential pages
- Know how to place an order and schedule delivery
- Know how to access Nanopore protocols
- Navigate the site and bookmark protocols
- Be able to switch between sequencing formats (e.g. flongel/MinION)
- Know how to estimate the ease or difficulty of sequencing experiments
- Take notes during the workshop and compare with protocol time estimates
- Use product pages to estimate costs
- Know how to estimate the ease or difficulty of analysis options
- Take notes during the workshop and align with your level of computational skills
- Know which analyses are challenging but worth learning
Group summary self-assessment
- Posted on last day of workshop
Evaluation and feedback
- Link available after workshop