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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Friday, June 30 • 15:20 - 16:35
D02: Improve Genome Annotation Accuracy through Manual Annotation in Apollo

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Apollo Poster

Authors

Nathan Dunn 1*, Monica Munoz-Torres 1, Deepak Unni 2, Eric Rasche 3, Eric Yao 4, Ian Holmes 4, Christine Elsik 2, Suzanna Lewis 1

1 : Lawrence Berkeley National Lab  (LBNL), Lawrence Berkeley National Lab 717 Potter Street Berkeley, CA 94710 -  United States
2 : Division of Plant Sciences, University of Missouri, 52 Agriculture Lab, Columbia, MO 65211 Columbia, MO 65211 -  United States
3 : Center for Phage Technology, Texas A&M University  (CPT), 2128 TAMU College Station, TX USA 77843-2128 -  United States
4 : Department of Bioengineering, University of California, Berkeley  (UC Berkeley), 119 California Hall Berkeley, CA 94720-1500 -  United States* : Corresponding author


Abstract
Modern genome annotation projects have increasingly involved working with less than perfect data on large and likely geographically disparate teams with more complex workflows. Galaxy excels at managing complex workflows that drive genome annotation projects. However, many times work groups skip this important step, which can be used to visually validate data and correct structural errors, sometimes between 10-30% of annotations.

Apollo is a web-based manual genome annotation tool built on top of the powerful JBrowse genome viewer that can be scaled to multiple genome projects and annotators. Apollo allows for collaborative, real-time editing, similar to Google Docs, and can be integrated within annotation workflows via a full suite of web-services (http://icebox.lbl.gov/Apollo2/WebServices/). To this end, it has been integrated within Docker (https://github.com/GMOD/docker-apollo) as well as Galaxy (https://github.com/GMOD/docker-compose-galaxy-annotation) and as part of a larger consortium of annotation projects (https://github.com/galaxy-genome-annotation/).

Current ongoing projects include support for variant curation and visualization of predicted effects as well as coordinate transformation. Coordinate transformation will allow collapsing of intra- (introns) and inter-genic (space between annotations) to focus attention on data-rich regions. Additionally, it will allow assembly of virtual scaffolds to allow annotation over poorer assemblies.

Find out more: http://genomearchitect.org.


Presenters
avatar for Nathan Dunn

Nathan Dunn

Lead Software Engineer, Lawrence Berkeley National Laboratory
Lawrence Berkeley National Lab (LBNL)



Friday June 30, 2017 15:20 - 16:35
Le Corum Le Corum

Attendees (5)