ERGA at the EMBO course in genome sequencing, assembly, curation, and downstream analyses

This September, the heart of Tuscany beat to the rhythm of genomics!  From the 8th to 12th September 2025, Florence, Italy, welcomed researchers from around the globe for the third edition of the EMBO Practical Course on Genome Sequencing, Assembly, Curation, and Downstream Analyses. This week-long event explored the entire workflow of reference genome projects - from sample preparation to sequencing, assembly and annotation and provided a key opportunity to showcase ERGA and how its collaborative infrastructures and shared standards support the generation of high-quality reference genomes across Europe.

EMBO course instructors and participants enjoying a moment together in front of Florence’s Basilica di Santa Croc

The course was designed for action. Participants worked hands-on with real datasets - PacBio HiFi, Oxford Nanopore, Illumina Hi-C and RNA-seq - to perform de novo assembly, scaffolding, haplotig purging, and genome annotation within the Galaxy platform, using the Training Infrastructure as a Service (TIaaS). Beyond technical exercises, the course offered insights into reproducible workflows, pangenome development, and AI-assisted functional annotation. ERGA workflows and tools drew particular interest, showing how standardized approaches can streamline genome projects and make high-quality genomic data widely accessible. Participants at all career stages left with new knowledge and skills to apply these cutting-edge practices in their own research.

This edition of the EMBO course was organized by Claudio Ciofi (University of Florence, IT) and Giulio Formenti (The Rockefeller University, US; ERGA Council member for Italy). The co-organizers and invited speakers included Aureliano Bombarely (IBMCP/CSIC, ES; ERGA Council member for Spain), Silvia Manrique (CSIC, ES), Jean-François Flot (Université libre de Bruxelles, BE), Nadège Guiglielmoni (University of Cologne, DE), Astrid Böhne (Museum Koenig Bonn, DE), Tom Brown (Leibniz Institute for Zoo and Wildlife Research, DE; Chair of the ERGA IT Committee), Kirsty McCaffrey (The Rockefeller University, US), Marco Sollitto (University of Florence, IT), Alice Mouton and Björn Grüning (University of Freiburg, DE), with assistance from Camilla Reginatto De Pierri (University of Florence, IT; Chair of the ERGA TKT Committee).

Text by Camilla Reginatto De Pierri, from the ERGA Training & Knowledge Transfer Committee