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Tuesday, June 28 • 3:10pm - 4:25pm
P11: Apollo: Collaborative Manual Annotation for Genomic Sequencing Projects

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Poster    doi:10.7490/f1000research.1112335.1

Authors

  • Nathan Dunn, Berkeley Bioinformatics Open-source Projects Lawrence Berkeley National Laboratory
  • Monica Muñoz-Torres, Berkeley Bioinformatics Open-source Projects Lawrence Berkeley National Laboratory
  • Colin Diesh, University of Missouri
  • Deepak Unni, University of Missouri
  • Eric Rasche, Department of Biochemistry and Biophysics, Texas A&M University
  • Eric Yao, University of California Berkeley
  • Ian Holmes, University of California Berkeley, 
  • Chris Elsik,  University of Missouri
  • Suzie Lewis,  Berkeley Bioinformatics Open-source Projects Lawrence Berkeley National Laboratory

Abstract

Manual annotation is a crucial step in the annotation portion of a genome sequencing project. It enables curators to improve automated gene predictions by visually comparing a variety of experimental evidence tracks from different sources to more accurately represent the underlying biology.

Apollo is a web-based genome annotation editor that allows curators to manually revise and edit genomic elements. It provides a reporting structure for annotated genomic elements and an ‘Annotator Panel’ that allows users to quickly browse the genome and its annotations. Users can manually edit the structure of a genomic element as well as add metadata, including references to other databases and functional assignments with specific lookup support for Gene Ontology (GO) terms.

Apollo is currently being used in over one hundred genome annotation projects around the world, ranging from annotation of a single species to lineage-specific efforts supporting annotation for dozens of organisms at a time. Collaborators are able to visualize each others changes in real time (similar to Google Docs), restrict access to annotations depending on the role of users and groups within the community, and share tracks of evidence data with the public. Finally, users are able to export their manual annotations via FASTA, GFF3, the Chado database schema, and web services. Lastly, Apollo is available for integration with Galaxy via Docker, allowing users to run genome analyses sequencing using the Galaxy platform.

Apollo is an Open-Source project. Further details and code are available at http://genomearchitect.org/. 

Presenters
avatar for Nathan Dunn

Nathan Dunn

Lead Software Engineer, Lawrence Berkeley National Laboratory
I primarily work on the Apollo project, a web-based genome editor used for real-time collaborative manual curation, AKA Google Docs for genome editing. Apollo is built using JBrowse as our genomic viewer. http://genomearchitect.org https://github.com/GMOD/Apollo We use Grails + GWT + Angular (in addition to the JBrowse stack). I'm a scientific programmer having worked in a variety of domains including biology, psychology, automated speech... Read More →


Attendees (7)