Apollo: collaborative and scalable manual genome annotation

Manual refinement of automated gene predictions using experimental evidence is a crucial step for improving the quality of a genome's annotation. Apollo, which utilizes the JBrowse genome browser, is a web-based genome annotation editor used by well over one hundred annotation projects. Annotation changes are reflected in real-time (like Google Docs), which facilitates distributed curation efforts. A single Apollo server can scale to support multiple genome projects and regulate access to multiple curators via fine-grained permissions. Apollo has been successfully integrated with Galaxy via Docker, and externally via its web-services, allowing the community to refine predicted genome elements generated via Galaxy workflows. Annotated genomic elements may be exported as FASTA, GFF3, or as a Chado database. We introduce two important features nearing completion. The first is variant annotation, which provides both a way to annotate and visualize variants as well as to visualize individual and combined effects of each variant on a given annotation. The second is coordinate transformation, which allows the visualization of two or more genomic regions, from the length of entire chromosomes to just a few exons, within an artificially constructed “assemblage”. This facilitates annotation of genomic features split across two or more regions of a fragmented assembly, while informing potential improvements to the genome assembly in the process. Additionally, inter- and intragenic regions can be hidden to focus on regions of interest. For example, bringing the sequences of exons separated by thousands of base-pairs to be shown adjacently. Learn more at  http://genomearchitect.org/ .