 Refining Genome Annotations with Apollo Before diving into this slide deck, we recommend you to have a look at the following. How to visualize your genome after automated annotations have been performed? How to manually annotate genome after automated annotations have been performed? How to evaluate and visualize annotated genomic features? How do I collaborate when doing genome annotation? Load a genome into Galaxy. View annotations in Jbrows. Learn how to load Jbrows data into Apollo. Learn how to manually refine genome annotations within Apollo. Export refined genome annotations. Annotating a genome means positioning features along the sequence of a genome. Here we focus on genes. We are interested in their positions and functional annotation like their name of their function. Many software tools and pipelines exist to automatically perform the annotation of a new genome sequence. For example Prokka or Maker are widely used and tutorials are available on the GTN to learn how to use them. Unfortunately, automatic annotations are rarely perfect. Assembly errors can cause fragmented annotations. Annotation tools have difficulties annotating genes when evidence is like Rnasek are lacking or too noisy. Performing a manual curation step after automatic annotation allows to improve annotation quality. It is a way to make use of a researcher's expertise and to integrate more knowledge to improve gene structures and functional annotation. Apollo is a web application specifically designed for the manual curation of annotations. You can see Apollo as the Google Docs of annotation. It is a multi-user, real-time, collaborative environment. Users can easily change the structure of genes and add functional annotation like gene names of gene ontology terms. It is based on ch-brows. Ch-brows is for visualizing genomes while Apollo adds the editing capabilities. Within Apollo, you can easily change the structure of genes based on evidence tracks. Apollo offers an interactive interface to help you add functional annotation. Apollo is a multi-user environment, which means multiple users can log in at the same time, make changes, and see changes of other users in real time. Apollo keeps track of every action performed on each gene in a history. You can revert any change at any time. Apollo is now tightly integrated with Galaxy, which allow to integrate the manual curation process in a complete Galaxy-based analysis workflow. Within Galaxy, you can start by assembling a new genome, then aligning as many evidence tracks as possible, like UNASIC data. You can then continue with an automatic annotation step. With Prokka or Maker for example, then you can generate a ch-brows instance representing all the data you have generated and loaded into Apollo. Apollo lets you perform the manual curation in collaboration with any other colleague you invite to help you. Finally, when you are satisfied with your changes, you can export them to your Galaxy history and continue other analyzes. At any time later you can come back to Apollo to continue improving the annotation based on new experiment results. By default you are the only one having access to genomes you load into Apollo. A specific module of the Apollo Galaxy bridge allows you to open the access to a genome to any other Galaxy user. You can now follow the Apollo tutorial to learn how to use it in real life. Apollo is the Google Docs of the genome annotation world, real-time collaborative genome annotation. Apollo allows a group to view and manually refine predicted genome annotations. Use Apollo to edit annotations within your group. Export manual annotations as GFF3. Thank you for watching.