Case Study: Institute of Tropical Medicine Antwerp accelerates mpox genomic research with Seqera Nextflow

ITM Antwerp leverages Nextflow to obtain breakthrough clinical research results

The Institute of Tropical Medicine Antwerp (ITM Antwerp) needed to rapidly sequence and analyze patient samples to help contain the 2022 global mpox outbreak, but lacked an in-house PCR confirmation process for early suspects and a whole-genome sequencing workflow for high-resolution research. Seqera’s Nextflow platform was used to build a portable, reproducible custom pipeline that could support outbreak investigation and molecular epidemiology.

Using Seqera’s Nextflow, ITM Antwerp developed and deployed a custom pipeline for Oxford Nanopore Technologies sequencing, enabling rapid analysis on local hardware and future portability to clusters or cloud environments. The solution helped confirm the Belgian index case through metagenomic sequencing, identify the outbreak variant, and support follow-on studies of asymptomatic, post-vaccination, and breakthrough infections, while enabling faster sharing of genomes with the global research community.

Institute of Tropical Medicine Antwerp

Antonio Mauro Rezende

Researcher