Reference genomes are becoming a new fundamental tool in biodiversity and evolutionary research and as a result, the number of reference genome initiatives is increasing, as demonstrated by the growing number of international initiatives to make genomes available across the tree of life, such as the Earth BioGenome Project. Training and access to knowledge on genome assemblies are becoming critical for the whole scientific community.
After the successful first edition of the EMBO course in Bruxelles at the Université libre de Bruxelles in September 2022, the second edition of the EMBO course on genome sequencing, assembly, and downstream analyses took place for a full week in Valencia in January 2024 within the Polytechnic University of Valencia (UPV). During this week, around 30 participants from everywhere in the world got equipped with theoretical knowledge and practical know-how to enable them to sequence their genome of interest and analyze it all the way to publication. This course covered the whole life-cycle of a reference genome sequencing project, from library preparation, DNA sequencing to genome assembly, assembly evaluation and assembly improvement and all the way to annotation.
The workshop's participants, speakers and organizers
On the first day, the speakers covered topics such as the importance of vouchering and metadata and high-quality DNA to start a genome project, followed by a broad overview of sequencing methodologies and associated cost and how to design sequencing experiments. On the following days, participants followed practicals about de novo genome assembly, assembly scaffolding, haplotig purging and annotation using the Training Infrastructure as a Service (TIaaS) implemented in the European Galaxy Server. The participants worked on PacBio HiFi and Oxford Nanopore datasets, Hi-C reads and Illumina RNA-seq coming from a nematode species belonging to the Panagrolaimidae family. The last few days, the speakers also gave enlightening talks about the importance of Galaxy for reproducible science, the future of pangenomes, the presence of reference genome initiative in the UK, in Europe, and in the US as well as the use of IA to infer functions of unknown protein. All the materials related to the course will be available in the upcoming ERGA Knowledge Hub.
Meet our nematode Propanagrolaimus JU765 kindly provided by Nadège Guigliemoni (University of Cologne, Germany)
The invited speakers for this course were Olga Vinnere Petterson (Uppsala University, SE), Rosa Fernández (Institute of Evolutionary Biology (IBE) (CSIC-UPF), ES), Kamil Jaron (Wellcome Sanger Institute, UK), Jennifer Leonard (Doñana Biological Station - CSIC, ES) and Linelle Abueg (The Rockefeller University, US).
This EMBO course was organized by Aureliano Bombarely (Institute of Plant Molecular and Cellular Biology (IBMCP)(CSIC-UPV), ES) , Silvia Manrique (Valencia Polytechnic University, ES), Giulio Formenti (The Rockefeller University, US), Jean-François Flot (Université libre de Bruxelles, BE), Alice Mouton (University of Florence, IT), Nadège Guiglielmoni (University of Cologne, DE).
Text by Alice Mouton
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