Peer-reviewed Publications

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    Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome
    (ACM, New York, NY, 2015-07-26) Wu, Le-Shin; Ganote, Carrie; Doak, Thomas; Barnett, William K.; Mockaitis, Keithanne; Stewart, Craig A.
    Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non- model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems, bioinformatic support for determining the appropriate method to analyze a given dataset, and practical assistance in running computations. We demonstrate that a sufficient supercomputing resource and good workflow design are elements that are essential to large eukaryotic genomics and transcriptomics projects such as the complex transcriptome of loblolly pine, gene expression data that inform annotation and functional interpretation of the largest genome sequence reference to date.
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    National Center for Genome Analysis Support Leverages XSEDE to Support Life Science Research
    (ACM, 2013-07-23) LeDuc, Richard D.; Wu, Le-Shin; Ganote, Carrie L.; Doak, Thomas; Blood, Philip D.; Vaughn, Matthew