GCC 2017

➔ Slides (doi: 10.7490/f1000research.1114357.1)

Authors
Nathan Dunn, Lawrence Berkeley National Lab (LBNL)
Monica Munoz-Torres, Lawrence Berkeley National Lab (LBNL)
Deepak Unni, Division of Plant Sciences, University of Missouri
Eric Rasche, Center for Phage Technology, Texas A&M University (CPT)
Eric Yao, Department of Bioengineering, University of California, Berkeley (UC Berkeley)
Ian Holmes, Department of Bioengineering, University of California, Berkeley (UC Berkeley)
Christine Elsik, Division of Plant Sciences, University of Missouri
Suzanna Lewis, Lawrence Berkeley National Lab (LBNL)


Abstract
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/.