23rd-25th March 2026

This intensive 3-day online course provides participants with a complete overview of Nanopore sequencing for environmental DNA (eDNA) metabarcoding. The course blends lectures on laboratory workflows (sample handling, PCR, library preparation, sequencing) with practical bioinformatics sessions, guiding participants through the full process from experimental design to biodiversity insights. Participants will gain the theoretical and practical knowledge needed to implement Nanopore-based eDNA projects in their own research.

Designed for researchers, ecologists, and bioinformaticians interested in:

     - Leveraging portable sequencing technologies for field studies.
     - Conducting biodiversity assessments using eDNA.
     - Developing or enhancing bioinformatics pipelines for metabarcoding.

By the end of the course, participants will be able to:  

• Understand each stage of the Nanopore eDNA lab workflow, from sampling to sequencing.  

• Recognise common pitfalls and troubleshooting strategies in molecular work.  

• Process Nanopore data (basecalling, filtering, clustering, taxonomic assignment).  

• Analyse biodiversity patterns with R, including alpha/beta diversity and ordination.  

• Evaluate how lab and bioinformatics workflows integrate into eDNA metabarcoding studies.  

Day 1 – From Sample to DNA Extract - 2-6 PM Berlin time

• Lectures

  • eDNA field sampling strategies and contamination controls

  • Preservation and extraction methods (filtration, precipitation, silica-column, magnetic beads)

  • PCR amplification strategies for eDNA metabarcoding (primer choice, blocking primers, indexing)

  • Common lab challenges: low DNA yield, inhibitors, contamination, PCR bias

• Hands-On Practical (Bioinformatics)

  • Exploring raw Nanopore files (FAST5/FASTQ)

  • Running basecalling and demultiplexing

  • Generating initial quality control reports

Day 2 – From DNA to Nanopore Libraries - 2-6 PM Berlin time

• Lectures

  • Nanopore sequencing kits for amplicon and metabarcoding studies

  • Barcoding and multiplexing strategies

  • Flow cell preparation, loading, and run monitoring

  • Real-time sequencing outputs and troubleshooting sequencing runs

• Hands-On Practical (Bioinformatics)

  • Filtering and trimming Nanopore reads

  • Error correction and read clustering

  • Visualising read length distributions and quality improvements

Day 3 – From Reads to Biodiversity Insights - 2-6 PM Berlin time

• Lectures

  • Taxonomic assignment workflows (alignment strategies and database selection)

  • MOTU/OTU generation and ecological interpretation

  • Integrating laboratory and computational workflows in eDNA projects

  • Case studies from conservation and biodiversity monitoring

• Hands-On Practical (Bioinformatics)

  • End-to-end workflow: filtered reads → MOTU table → community analysis

  • Calculating and interpreting diversity metrics (alpha and beta) in R

  • Producing publication-ready biodiversity plots

• Wrap-Up Discussion

  • Strengths, limitations, and future directions of Nanopore eDNA sequencing

  • Open Q&A and participant project discussions