Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources (Poster)

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Plant and Animal Genomics 2018


Whole genome reference and functional genomics projects most often benefit from a diversity of expertise and the integrated contributions of multiple research groups. The importance of web-enabled data sharing and open access software to progress in genome research is indisputable. Dissemination of genome resource information through internet-based resources, especially customizing and encouraging the optimal use of analysis tools to serve a specific research community, often lags behind data generation. This lag can inhibit biological interpretations and downstream experimentation, much of which should be undertaken before a genome resource project is completed. File systems for storing data and analysis outputs of today’s project standards must be large and secure, and must offer sustained access to fulfill the hosting requirements an active and dispersed research community needs. Users must interact with a computing resource powerful enough to get their jobs done, and sites must be expandable and flexible to accommodate a growing demand for intra-genera comparisons and pan-genomics of a species. We have been using NSF XSEDE computational resources including Jetstream along with the High Performance Computing systems of Indiana University to meet these challenges for a variety of collaborative plant genomics studies. Currently these efforts are impacting metabolic gene discovery in the tetraploid Arachis hypogaea and whole genomic reference studies of the tetraploid Coffea arabica and its diploid progenitors. Here we show practical examples of XSEDE resource use and development that may benefit other genomic research groups seeking to increase the effectiveness of their computing and collaboration.



bioinformatics, hardware, transcriptomics, web, visualization, JBrowse


Ganote, C., S. Sanders, L. Wu, T. Doak, and K. Mockaitis. (2018). Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources (Poster). Plant and Animal Genomics 2018, San Diego, CA. Retrieved from


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