A Genome Sequence Analysis System Built with Hypertable

Deep genome sequencing has revolutionized the fields of biology and medicine. Since January 2008, the capacity to generate sequence data has increased exponentially, far outpacing Moore's Law. The emergence of scalable NoSQL database technologies has made the analysis of this vast amount of sequence data not only feasible, but cost effective. The University of California at San Francisco UCSF-Abbott Viral Detection and Discovery Center, led by director Charles Chiu, MD, PhD, Taylor Sittler, MD and the Hypertable development team have embarked upon a project to build a scalable software platform to facilitate deep sequencing analysis in diagnostic microbiology, transcriptomic analysis, and clinical / environmental metagenomics, areas for which existing commercial and academic solutions are sorely lacking. Doug Judd, the original creator of Hypertable, will present an overview of this genome sequencing analysis system. The presentation will cover the following topics: Rationale for choosing NoSQL Schema design Sources and description of input data Algorithms for generating and querying lookup tables Table sizes and compression ratios Lessons learned during system deploymentRead less