Apollo: Collaborative Manual Genome Annotation with Visual Predictions

Manual curation is crucial to improving the quality of the annotations of a genome. It enables curators to refine automated gene predictions using experimental data and aligned predictions from closely related organisms to more accurately represent the underlying biology. Apollo is a web-based genome annotation editor that allows curators to manually edit the structure and function of predicted genomic elements. Changes are reflected in real-time to all users and aggregated in a revertible, visual history of structural edits. Annotations can be exported as FASTA, GFF3, or Chado.

A single Apollo server can be scaled to support multiple genome projects and curators — whose access can be controlled with fine-grained permissions. Apollo can be integrated easily into workflows using our large suite of web services, which has facilitated integration within the Galaxy platform.

Two major undertakings are currently underway. First, is visualization of variant data to annotate their predicted effects, primarily on coding regions. Second, is the transformation of genomic coordinates into synthetic regions to allow hiding (visual genome folding) of intra- and intergenic regions, providing a more information-rich visualization of the genome as well as the ability to combine scaffolds that will allow annotation of genomic features split across two or more regions of a fragmented assembly.

Apollo is used in over one hundred genome annotation projects around the world, ranging from annotation of a single species to lineage-specific efforts supporting the annotation of dozens of species at a time. http://genomearchitect.org/