GenEpi-BioTrain - Virtual Training 27 - Clinical application of Nanopore-based 16S metagenomic sequencing for diagnostics

Topic outline

• Welcome to the virtual training on clinical application of Nanopore-based 16S metagenomic sequencing for diagnostics

  Welcome to the virtual training on clinical application of Nanopore-based 16S metagenomic sequencing for diagnostics

  Course description

  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.

  Target audience

  The intended audience are bioinformaticians, microbiologists, molecular biologists or public health professionals with:

  • Introductory knowledge of 16S sequencing;
  • Introductory experience using the terminal;
  • Intermediate experience with bioinformatics;
  • An interest in the clinical use of Oxford Nanopore for diagnostic 16S rDNA sequencing.

  Background & Rationale

  Diagnostic 16S rDNA sequencing is useful to detect and identify bacteria that are difficult to culture or have reduced viability due to antibiotic treatment. Using Next Generation Sequencing (NGS) for diagnostic 16S rDNA analysis also enables analysis of polymicrobial specimens, whereas Sanger sequencing detects only the dominating species.

  This training highlights the utility of NGS-based 16S rDNA sequencing in a clinical setting and focuses on the skills required to locally implement a bioinformatics pipeline for Oxford Nanopore sequencing, prioritising short turnaround times.

  The training addresses the following questions:

  • How can NGS-based 16S rDNA sequencing be applied in a clinical diagnostic setting
  • Why Oxford Nanopore is useful for 16S rDNA sequencing
  • How to set up and run a pipeline to process 16S rDNA Nanopore sequencing data
  • How to interpret and evaluate 16S rDNA sequencing results from the EMU software

  Format

  This virtual training consists of two half-day sessions held on the mornings of Monday 1 June, and Friday 5 June 2026, from 09:00 to 12:30 (CET).

  Outline

  Session 1: Background of 16S rDNA sequencing and analysis

  Part 1: Oxford Nanopore based 16S rDNA sequencing

  Part 2: The Emu tool and the Trana pipeline

  Part 3: Introduction to exercises + short Q&A

  Session 2: Interpretation of results

  Part 1: Reporting, thresholds and alignment quality metrics

  Part 2: Clinical interpretation and evaluation

  Part 3: Recap of exercises and Q&A

  • PagePresenters' biography
  • PageVirtual training organisation credits
  • PageLegal terms and conditions
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  Aim and objectives

  Aim and objectives

  Across two half-day sessions, participants will gain an overview of 16S rDNA sequencing using Oxford Nanopore technology and its application in diagnostic bacterial typing. The training combines presentations on sequencing methodology, bioinformatic tools, and result interpretation with hands-on exercises using Emu, Trana and TranaVy. This provides participants with both the theoretical foundation and practical skills needed to carry out Nanopore-based 16S rDNA sequencing analysis projects.

  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.
• Prepare for the Virtual Training

  Prepare for the Virtual Training

  Access to a computer with the Linux operating system is required to install and run all the tools included in the exercises.

  See the link to instructions below, for more details.

  • PageInstructions
• Session 1: 16S background and analysis pipeline

  Session 1: 16S background and analysis pipeline

  Time CEST	Session	Intended Learning Outcomes
  09:00-09:15	ECDC introduction Presenters: Priyanka Nannapaneni, ECDC	Greeting of participants, presentation of GenEpi-BioTrain, code of conduct, get to know the participants, get to know the trainer
  09:15-10:00	Lecture: Background: 16S biology, Nanopore sequencing Presenters: Samuel Lampa, Anna Norén	Get the background knowledge needed to understand why 16S rDNA sequencing is used and how it compares to other approaches like whole-genome sequencing and untargeted metagenomics.
  10:00-10:15	Coffee Break
  10:15- 11:00	Lecture: Tools for analysis of Nanopore 16S rDNA data: EMU, the TRANA pipeline and the TranaVy reporting tool. Presenters: Samuel Lampa, Anna Norén	Learn about available open-source tools that can be used for analysis of 16S rDNA Nanopore data.
  11:00-11:15	Coffee Break
  11:15-12:00	Tutorial: Installing and running Emu and Trana, and Extracting unassigned reads. Case presentation.	Getting hands-on experience with the Emu tool, the Trana pipeline and the TranaVy reporting tool. Be able to troubleshoot problematic results by extracting selected reads from the raw alignment in Emu.
  12:00-12:30	Time to work on exercises and Q&A

  • Opening of session 1

  • Part 1 - Background: 16S biology, Nanopore sequencing 

    
    

  • FileBackground: 16S biology, Nanopore sequencing
  • Part 2 - Tools for analysis of Nanopore 16S rDNA data: EMU, the TRANA pipeline and the TranaVy reporting tool 

    
    

  • FileTools for analysis of Nanopore 16S rDNA data: EMU, the TRANA pipeline and the TranaVy reporting tool
  • Part 3 - Installing and running Emu and Trana, and Extracting unassigned reads. Case presentation.   

    
    

• Course Exercises

  Course Exercises
  • URLPreparations for the exercises
  • FileExercises introduction, caveats and further resources
  • URLExercise 1: Install and test run Emu [External link]
  • FileExercise 1: Install and test run Emu [PDF]
  • URLExercise 2: Troubleshoot Emu output [External link]
  • FileExercise 2: Troubleshoot Emu output [PDF]
  • URLExercise 3: Install and run the Emu-based Trana pipeline [External link]
  • FileExercise 3: Install and run the Emu-based Trana pipeline [PDF]
• Session 2: Interpretation of results

  Session 2: Interpretation of results

  Time CEST	Session	Intended Learning Outcomes
  09:00-09:15	ECDC introduction Presenters: Priyanka Nannapaneni, ECDC	Greeting of participants, presentation of GenEpi-BioTrain, code of conduct, get to know the participants, get to know the trainer
  09:15-10:00	Lecture: Reporting of results - Raw alignment metrics vs Consensus sequence based metrics Presenters: Anna Norén, Samuel Lampa	Ability to use the raw alignment metrics available in the TranaVy tool to assess quality and reliability of individual species' abundance estimations.
  10:00-10:15	Coffee Break
  10:15- 11:00	Lecture: Clinical interpretation of results Presenters: Dr. Elin Loo	The ability to understand the principles used for clinical interpretation of 16S rDNA sequencing results, such as comparing with negative control, the use of spike for normalising abundances and identifying clinically relevant pathogens.
  11:00-11:15	Coffee Break
  11:15-12:00	Recap of exercises	Solidifying hands-on skills to run common open source tools for Nanopore-based 16S rDNA sequencing and access its results, as well as troubleshoot problematic results.
  12:00-12:30	General discussion and Q&A

  • Session 2 - Opening
  • Part 2 - Reporting of results - Raw alignment metrics vs Consensus sequence-based metrics 

     
    
  • FileReporting of results - Raw alignment metrics vs Consensus sequence based metrics
  • Part 3 - Clinical interpretation of results
  • FileClinical application and interpretation
  • Part 4 - Recap of exercises  

    
    

• Contacts

  Contacts

  For any questions regarding the this webinar series, please use the discussion forum.

  If you have questions regarding other training initiatives please contact: courses@ecdc.europa.eu.

  If you have technical issues please contact the ECDC Service Desk at servicedesk@ecdc.europa.eu.