Apollo: Improving Collaborative Genome Curation

New genomics tools lead to better understanding organisms in ways previously unthinkable. Apollo enables collaborative, real-time curation (akin to Google Docs) of genomic elements using structural and experimental information. Built on top of JBrowse, Apollo is composed of a web-based client, an annotation-editing engine, and a server-side data service. Users can visualize gene models, protein alignments, and expression and variant data to conduct structural and/or functional annotations. In our most recent release, version 2.0.x, the improved architecture allows users to more easily query data and build extensions, supports multiple organisms per server, and allows additional types of sequence annotations based on Sequence Ontology. The new, removable side-dock offers detailed view of annotations, sequences, and organisms, a new reporting structure, and WebSocket support to improve real-time communication. The new Grails framework (Spring / Hibernate / Groovy) in the server more robustly scales a single server over multiple organisms while better supporting additional curators. Apollo’s secure REST API is exposed, allowing genomic features to be injected into Apollo from an automated curation process or organization-specific metadata to be extracted directly from Apollo using a SQL query or REST. The new version offers improved features, including the ability to bring together 2 or more scaffolds in order to annotate genes split across them, and increases the ability to customize and integrate Apollo into the curation pipelines of modern sequencing projects. Here we introduce the new architecture, highlight advantages for users, and detail our future plans. Project Website: http://genomearchitect.org/