This training provides an overview of 16S rDNA sequencing with Oxford Nanopore for diagnostic bacterial typing. Participants learn the core principles of 16S rDNA sequencing, the basics of Oxford Nanopore technology, commonly used analysis tools, and key approaches for interpreting results. The training provides the essential background needed to carry out Nanopore-based 16S rDNA analysis projects. Hands-on exercises using the Emu and Trana pipelines, along with targeted read extraction for troubleshooting, reinforce the presentations and build practical skills for effective  Nanopore-based 16S rDNA sequencing analysis.

 Dates: Monday 1 and Friday 5 June 2026. 

 Duration: Two half-days 09:00-12:30 CET. 

Location: Online - Find the link after enrolment. 

Audience: The intended audience are bioinformaticians, microbiologists, molecular biologists or public health professionals with some computational experience.

Objectives - Upon completing this course, participants will be able to:

• Understand the advantages and limitations of 16S rDNA metagenomics in clinical diagnostics;
• Set up and run an EMU-based pipeline locally or on a GridIon instrument;
• Understand the resource requirements for running the pipeline;
• Have a basic understanding of the EMU algorithm and the main differences from other approaches;
• Have a good understanding of how to interpret and report sequencing results to the treating physician;
• Have the hands-on skills to extract and isolate selected reads for downstream troubleshooting and quality assessment.

Participation: This course is open for public enrolment.