Twinning visit regarding Next-Generation Sequencing (NGS) and bioinformatics, Stockholm, 11-13th November, 2025
We are pleased to invite applications for our upcoming Twinning Visit on Whole‑Genome Sequencing (WGS) of human monkeypox virus (MPXV) using Oxford Nanopore Technologies. The twinning will take place from 11 to 13 November in Stockholm, Sweden and is hosted by the Public Health Agency of Sweden.
The training is aligned with the Consortium’s capacity-building objectives and tailored based on survey results from network members. It includes wet-lab practice, bioinformatics analysis, and the integration of sequencing data into public health surveillance. Travel and accommodation costs will be imbursed and the twinnig visit is free of charge.
The training aims to achieve the following learning objectives:
Upon successful completion of the visit, participants will be able to:
Knowledge
- Describe the core principles and workflow of Oxford Nanopore Technologies (ONT) sequencing, including its applications in pathogen genomics.
- Explain the theoretical basis of tiled‑amplicon whole‑genome sequencing for DNA viruses such as hMPXV.
Skills
- Carry out laboratory steps—including tiled amplification, Nanopore library preparation, flow cell loading and sequencing run setup—to generate raw reads for hMPXV.
- Execute a standardised bioinformatics workflow (demultiplexing, trimming, mapping, consensus calling) and assess quality metrics in a Linux environment.
- Assign clade and generate a basic phylogenetic placement using Nextclade.
Competence
- Interpret consensus genomes in the context of genomic surveillance and communicate findings to public health stakeholders.
- Draft an implementation plan for adopting the workflow at their home institute, including QC checkpoints and data‑sharing procedures.
Target participants
Professionals with good molecular biology experience, employed at an institution that operate – or plan to establish Nanopore sequencing facilities.
How to apply
Send your application to the e-mail EURL-PH-ERZV@folkhalsomyndigheten.se, including:
- A brief motivational letter (≤ 1 page)
- A short form CV (≤ 2 pages)
- A letter of recommendation from your direct manager
- In case you are not members of the disease network supported by the EURL-PH-ERZV, you must have a letter of endorsement from the OCP for Microbiology or the NFP EVD.
Application deadline
30 August 2025.
We look forward to welcoming participants from across the network!
Logistical information
Date: 11-13th November 2025
Venue: Laboratories of the Public Health Agency of Sweden, Solna, Sweden.
Preliminary agenda
- Pre-visit online seminar 3 hours
- Day 1 – Theoretical foundations
- Day 2 – Wet-lab practicals and case studies
- Day 3 – Bioinformatics practicals and troubleshooting