Apollo: Democratizing genome annotation

Abstract

Genome annotation is the process of identifying the location and function of a genomes encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, Apollo is an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform.\n\nIn this paper we first outline some of Apollos newer user interface features, which were driven by the needs of this expanding genomics community. These include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible. O_LISource: https://github.com/GMOD/Apollo\nC_LIO_LILicense (BSD-3): https://github.com/GMOD/Apollo/blob/master/LICENSE.md\nC_LIO_LIDocker: https://hub.docker.com/r/gmod/apollo/tags/, https://github.com/GMOD/docker-apollo\nC_LIO_LIRequirements: JDK 1.8, Node v6.0+\nC_LIO_LIUser guide: http://genomearchitect.org; technical guide: http://genomearchitect.readthedocs.io/en/latest/\nC_LIO_LIMailing list: apollo@lists.lbl.gov\nC_LI