Genome Annotation and Other Post-Assembly Workflows for the Tree of Life

Rapid advances in genome sequencing technologies have resulted in an explosion of reference-quality genome assemblies across the tree of life. While these resources will be invaluable toward goals of species and biodiversity conservation, their application is limited when they lack accurate annotations of functional elements. The European Reference Genome Atlas (ERGA), the European node of the Earth Biogenome Project (EBP), aims to share resources and knowledge to create fully annotated reference genomes in a distributed manner, bringing together researchers worldwide with common goals and understandings. In the BioHackathon Europe 2023, we constructed and tested tools, pipelines, and workflows for annotating protein-coding regions in assembled genomes, evaluating performance across diverse non-model organisms and the usability of pipelines for newcomers. This required deploying tools across multiple compute environments, sharing genomic resources and expertise across institutes, and assessing workflow performance and input data requirements to achieve high-quality genome annotation. Here we present results from over 20 researchers in 8 time zones working toward robust genome-annotation workflows in eukaryotes.