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Open Access Publications from the University of California

GAViT: Genome Assembly Visualization Tool for Short Read Data

  • Author(s): Syed, Aijazuddin
  • Shapiro, Harris
  • Tu, Hank
  • Pangilinan, Jasmyn
  • Trong, Stephan
  • et al.

It is a challenging job for genome analysts to accurately debug, troubleshoot, and validate genome assembly results. Genome analysts rely on visualization tools to help validate and troubleshoot assembly results, including such problems as mis-assemblies, low-quality regions, and repeats. Short read data adds further complexity and makes it extremely challenging for the visualization tools to scale and to view all needed assembly information. As a result, there is a need for a visualization tool that can scale to display assembly data from the new sequencing technologies. We present Genome Assembly Visualization Tool (GAViT), a highly scalable and interactive assembly visualization tool developed at the DOE Joint Genome Institute (JGI).

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