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4/09PacBio SMRT Portal and Assembly

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  • Thu Apr 9, 9:00 am - 11:30 am
    138
    Cargill Building
    Series: Informatics
    This tutorial is part of the MSI/NSF Long-read assembly workshop being held on April 9, 2015. Separate registration for the entire event is required. See the description of the event and link to the registration form on the <a href="https://www.msi.umn.edu/events/genome-assembly-mini-symposium">MSI website</a>. Recent advances in long read sequencing have revolutionized genome assembly, enabling complete reconstruction of microbial genomes and significantly improved assemblies for higher organisms. This interactive tutorial introduces open source tools and workflows for analyzing, assembling, and interpreting Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing data. The workshop will primarily focus on PacBio’s SMRT Analysis graphical user interface (to be fully supported by MSI), but other command line tools for correction, assembly, and polishing of PacBio data will also be briefly introduced. Topics covered will include managing and importing raw SMRT cell data, adapter removal and subread filtering, SMRT cell loading and quality control, read self-correction and pre-assembly, de novo long read assembly with the hierarchical genome assembly process (HGAP), assembly polishing with Quiver, and base modification and methylation motif detection. Basic familiarity with the Unix command line is beneficial but not required. Example data will be provided, but attendees will have the opportunity to analyze their own PacBio data if available.