Building high-quality reference genome assemblies of eukaryotes

Workshop details
  • Date: Wed, September 14th
  • Time: 13:30 to 16:30 CEST
  • Format: Virtual
  • Nadège Guiglielmoni, Institut für Zoologie, Universität zu Köln, Cologne (Germany)
  • Joanna Malukiewicz, Deutsches Primatenzentrum, Göttingen, Germany and Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo (Brazil)
  • Lino Ometto, Department of Biology and Biotechnology, University of Pavia, Pavia (Italy)
  • Robert Waterhouse, Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne (Switzerland)

This workshop aims to introduce methods for chromosome-level genome assembly of eukaryote species using long reads and Hi-C, and to evaluate the quality of these assemblies


The field of genome assembly has been thriving with the continuous improvement of sequencing methods. These advances have prompted bold initiatives to generate high-quality genomes for Earth’s biodiversity, being coordinated in Europe by the European Reference Genome Atlas (ERGA) initiative and globally by the Earth BioGenome Project. Changing technologies and increasing volumes of data necessitate constant algorithmic innovations and developments to take advantage of the specificities of heterogeneous sequencing datasets. The combination of long reads and Hi-C have now become a gold standard for genome projects to yield reference chromosome-level assemblies, yet large eukaryote genomes remain challenging due to their variable levels of heterozygosity and repetitive content. This workshop aims to gather experts to summarise the latest advances in genome assembly, scaffolding, and assembly evaluation, and lead the discussions on scientific and technical challenges. This is motivated by needs in the community to exchange research ideas and share practical experiences of getting the best results from data generated by the latest technologies. The workshop is also motivated by a desire to engage computational biologists from further afield to bring their algorithmic expertise to the discussions and the task of genome assembly. The scope is focused on eukaryotic biodiversity which presents many different challenges in terms of sequencing and assembly, that the field as a whole is currently working to address.

Target Audience

Researchers who want to assemble genomes and to have an overview of the field, as well as bioinformaticians and computer scientists who could address algorithm issues

13:30 – 14:30Long-read assembly
Rayan Chikhi, Institut Pasteur, Paris (France)
14:30 – 15:30Assembly post-processing
Nadège Guiglielmoni, Universität zu Köln, Cologne (Germany)
Lyam Baudry, Université de Lausanne, Lausanne (Switzerland)
Ann M. McCartney, National Institutes of Health, Bethesda (USA)
15:30 – 16:30Finishing a genome assembly
Matthew Berkeley, Swiss Institute of Bioinformatics, Geneva (Switzerland)
Mathieu Seppey, Université de Genève, Geneva (Switzerland)
Tanja Schwander, Université de Lausanne, Lausanne (Switzerland)