SCGPM Seminar: Ravi Pandya, Microsoft Research

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James H. Clark Center

318 Campus Dr

Seminar Room S360

Stanford, CA 94305

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"Accelerating genomics in the cloud"

Ravi Pandya, Microsoft Research

Wednesday, March 15th
12:00 - 1:00PM
Clark S360 - Lunch provided

ABSTRACT: I will describe an optimized version of the Broad Institute best practices BWA/GATK pipeline that we have developed to run in the Microsoft Azure cloud as an easy-to-use web service. This pipeline gives similar accuracy to standard BWA/GATK, but can process a 30x whole-genome FASTQ into aligned BAM and VCF in a few hours instead of a day or more. We took the original BWA and GATK algorithms and combined them with the high-performance input/output and compute framework in our SNAP aligner, then rewrote key components of the algorithms for speed while retaining compatibility. We also built a scalable, reliable, secure cloud service to simultaneously process large numbers of genomes across a fleet of machines.

BIO: Ravi Pandya works in the Microsoft Genomics group on high-performance algorithms for genome alignment, assembly, and structural variation. He is one of the authors of the SNAP short-read aligner, which can produce high-quality genome alignments up to 10x faster than other state-of-the art aligners. He is also involved in the BeatAML collaboration led by Brian Druker’s lab at OHSU, to apply machine learning, predictive analytics, and systems biology to recommend personalized, targeted drug combinations for refractory leukemia patients.

ABOUT THE SCGPM: The Stanford Center for Genomics and Personalized Medicine (SCGPM) seeks to advance genomic technology so that someday both genetic and molecular profiling will become powerful and routine tools for predicting disease risk and monitoring and treating a wide range of pathologies. Towards this mission, the SCGPM serves to centralize and develop collaborative intellectual and technological resources that promote genomic research and analysis, predict drug response, educate physicians, and examine the ethics of personalized medicine. This includes large basic science projects such as ENCODE that decipher the human genome as well as clinical research projects such as the sequencing of cancer genomes and individuals with inherited diseases. Through these efforts, the Center aims to bring genomics to the clinic.

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The SCGPM supports the Genetics Bioinformatics Service Center, a SoM core facility for genomics research that provides a secure on-premise computing infrastructure, Google Cloud gateway, and bioinformatics consulting. The facilities are available to all faculty members at Stanford University.

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