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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 • 11:10 - 11:30
COMBAT TB: an integrated environment for Tuberculosis data analysis and surveillance

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Slides

Authors

Peter Van Heusden, South African National Bioinformatics Institute (SANBI)
Thoba Lose, South African National Bioinformatics Institute (SANBI)
Ziphozakhe Mashologu, South African National Bioinformatics Institute (SANBI)
Alan Christoffels, South African National Bioinformatics Institute (SANBI)


Abstract
Tuberculosis (TB), caused by the M. tuberculosis bacteria, continues to be one of the leading causes of morbidity and mortality in sub-Saharan Africa. TB surveillance in Africa requires computational tools at the sites where patients are being treated to facilitate rapid analyses of mycobacterial genomes. In 2016, under the auspices of the COMBAT TB project we have developed an integrated environment (the COMBAT TB Explorer) that allows researchers to interrogate their in-house data as well as interpret their data in the context of data available in the publicly available annotation of M. tuberculosis. We used the international Global Alliance for Genomic Health (GA4GH) variant model to implement genetic variant storage in Neo4J. Users can import variant collections and associated phylogenetic trees from Galaxy. All user data is available from a “My Data” view that allows examination of variants, trees and associate genome browser tracks and lists of genes associated with sequence variation. From the “My Data” view users can select variant collections and (using Galaxy) compute novel trees showing the phylogenetic relationship between samples and variant collections. A task queue allows jobs submitted via the Explorer interface to execute asynchronously, with the user notified when new data is available for viewing. The COMBAT TB environment (including the Explorer and Galaxy server environment) is available as a Docker container, with all code available on Github.

Presenters
PV

Peter Van Heusden

South African National Bioinformatics Institute (SANBI)



Friday June 30, 2017 11:10 - 11:30
Einstein Auditorium Le Corum, Level 0

Attendees (16)