2–5 November 2026: Training on Viral Whole Genome Sequencing and Bioinformatics using Oxford Nanopore Technologies, Stockholm

• Date: 2–5 November 2026
• Venue: Public Health Agency of Sweden (PHAS), Stockholm, Sweden

The training will take place from 2 to 5 November 2026 at the Public Health Agency of Sweden (PHAS) in Stockholm, Sweden. It will consist of a four-day in-person theoretical and practical course combining laboratory work and bioinformatics exercises.

Key topics

Viral whole genome sequencing and bioinformatics analysis using Oxford Nanopore Technologies (ONT).

The course combines lectures, laboratory sessions, and hands-on bioinformatics exercises covering the complete workflow for viral whole genome sequencing using ONT.

Participants will gain hands-on experience in:

• Viral genomic surveillance and sequencing strategies
• Amplicon-based sequencing workflows
• Amplicon PCR and library preparation
• Nanopore sequencing run setup and monitoring
• Basecalling and quality control of sequencing data
• Genome assembly and consensus sequence generation
• Introductory phylogenetic analysis
• Interpretation of genomic data and applications in outbreak investigations

The training also aims to support implementation of sequencing workflows within participating laboratories and promote collaboration and knowledge exchange across the EURL-PH-ERZV network.

To maintain an interactive learning environment, participation will be limited to six participants, allowing close supervision and practical work in small groups.

Target participants

Professionals with experience in molecular biology employed at an institution involved in molecular diagnostics, genomic surveillance, public health surveillance, or research, which operates or intends to implement sequencing activities.

What you need to know before applying

This course is hands-on from the first day. Participants will run interactive analyses with standard bioinformatics tools, write bash scripts, build Docker containers, and construct Nextflow pipelines. To keep up, you need a working knowledge of the Unix command line before you arrive.

You do not need to be an expert. You should be able to navigate the filesystem, move and edit files, and run basic commands without consulting a reference. If the command line is new to you, work through episodes 1–4 of the Software Carpentry Unix Shell lesson (swcarpentry.github.io/shell-novice) before the course. Set aside roughly three hours for this.

You will also need Docker Desktop installed and running on your laptop. Installation takes one to two hours and requires a reasonably up-to-date operating system. Full instructions are provided after you register.

No prior experience with Docker, Nextflow, or bioinformatics pipelines is expected; the course builds those skills from the ground up.

Participant selection

Applicants should provide a brief CV and a motivation letter. Applicants who are not members of the disease network supported by the EURL-PH-ERZ should also provide a letter of endorsement from the Operational Contact Point (OCP) for Microbiology or the National Focal Point (NFP) for Emerging Viral Diseases, and be affiliated with the same institution as the endorsing OCP or NFP.

Participants will be selected based on laboratory experience, current involvement in sequencing activities, and geographical representation across the EURL network.

How to apply

Applications are coordinated through the OCPs or NFPs within the EURL-PH-ERZV network.

If you are interested in participating, please contact your OCP or NFP for information about the application process and nomination procedure.

Application deadline: 31 August 2026.

We look forward to welcoming participants from across the network to Stockholm!

Training programme (Draft)

Day 1 – Introduction and theoretical background

• Introduction to the EURL-PH-ERZV training programme
• Overview of viral genomic surveillance
• Principles of whole genome sequencing
• Amplicon-based sequencing workflows
• Amplicon PCR preparation

Day 2 – Wet-lab training

• Overview of sequencing workflow
• Introduction to sequencing data analysis
• Library preparation for Nanopore sequencing
• Sequencing run setup and monitoring

Day 3 – Bioinformatics analysis

• Basecalling and initial data processing
• Quality control of sequencing data
• Genome assembly and consensus sequence generation
• Introduction to phylogenetic analysis

Day 4 – Interpretation and applications

• Interpretation of genomic data
• Application of sequencing data in outbreak investigations
• Discussion of implementation strategies in participating laboratories
• Course summary and feedback session