Galaxy Genome Annotation: Galaxy as a platform for the annotation of genomes

Galaxy Genome Annotation (GGA) is a project focusing on developments and resources to turn Galaxy into a complete and efficient platform for the structural and functional annotation of genome sequences. In this talk, we will present an update on the material produced by the GGA community in the last years on this topic. First, GGA has developed Galaxy tool wrappers for widely used, state-of-the-art annotation tools (e.g. Prokka, Maker, Braker, Funannotate, BUSCO, InterProScan, repeat masking tools) and Galaxy annotation workflows making use of these tools for real-life data analysis. This talk will give an overview of these developments, and discuss a few challenging issues that were encountered (e.g. complex dependencies, licensing, specific computing requirements). Another aspect of the GGA work is the integration of powerful genomics data visualizations directly within Galaxy, such as Circos, JBrowse (1 and 2) or GeneNoteBook. An important effort has also been carried out on the integration of more complex web applications, using specialized Docker images and Python libraries, such as Tripal or Apollo, a real-time, multi-user, collaborative manual curation of genome annotation, deployed on https://usegalaxy.eu/apollo . Based on all these results, training material was produced in the frame of the Gallantries project (Erasmus+), integrated into the Galaxy Training Network, and adopted by hundreds of students who attended the three GTN Smörgåsbord editions, and several other local training events. Put together, the various outcomes of the GGA project now enable scientists to perform complete genome annotation projects using Galaxy. Just as large scale sequencing projects (VGP, ERGA, Atlasea) are using Galaxy for genome assembly of thousands of genomes, GGA allows to go one step further by providing high quality, state-of-the-art Galaxy components for the annotation of these newly sequenced and assembled genomes.