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Workshop 1: Working with NGS Data: Tools and Techniques

Chair: Peter Hoyt, PhD, Oklahoma State University

Thursday March 6, 10AM - 5PM

    This workshop will consist of hands-on exercises prepared by Haibo Tang at the J. Craig Venter Institute (JCVI) using Next Generation Sequencing (NGS) data. Online tools will be introduced, but most exercises will be performed on OSU's new super computer: Cowboy.  Excercises in recent metabolomics methodologies will be given by Dr. Joshua Orvis (University of Maryland, Institute for Genome Sciences). The workshop will be suitable for beginners.  Dr. Dana Brunson of the OSU High-Performance Computing Center will present Basic Linux and Bash scripting commands to facilitate the exercises.

    Participants will acquire an iPLANT* user account to access the NGS applications hosted at the Texas Advanced Computing Center (TACC).  The workshop will cover several tools used for analyzing and optimizing both Roche-454 and Illumina 2^nd generation sequencing datasets.  The goal will be primarily introduction, not complete elucidation. The iPLANT examples will be wrapped in a facile GUI environment.  Exercises on Cowboy will be based on command-line operations.

    Participants should bring a laptop or tablet with current JAVA installed. Expect a rapid pace and plan accordingly.

*iPLANT, please see the organization website for more information: https://www.iplantcollaborative.org/