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GTC ON-DEMAND

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Abstract:
Base recalibration is a crucial step in data processing for DNA and RNA sequencing. Established in 2010 by our group in conjunction with the 1000 Genomes project, recalibrating the probability of error for each base in a genome based on counting observations and re-modeling the empirical error has proven to correctly down estimate the systematic errors made by the sequencing instrument allowing bayesian variant calling algorithms to make the most accurate choice. The task of counting observations in the entire genome is daunting and slow. In this talk we will show how we adapted the algorithm for GPU processing to improve the very long runtimes of this process and how the use of GPUs puts us one step closer to enable fast diagnostics of critical patients in need of a fast answer.
Base recalibration is a crucial step in data processing for DNA and RNA sequencing. Established in 2010 by our group in conjunction with the 1000 Genomes project, recalibrating the probability of error for each base in a genome based on counting observations and re-modeling the empirical error has proven to correctly down estimate the systematic errors made by the sequencing instrument allowing bayesian variant calling algorithms to make the most accurate choice. The task of counting observations in the entire genome is daunting and slow. In this talk we will show how we adapted the algorithm for GPU processing to improve the very long runtimes of this process and how the use of GPUs puts us one step closer to enable fast diagnostics of critical patients in need of a fast answer.  Back
 
Topics:
Life & Material Science, Big Data Analytics, Developer - Algorithms
Type:
Talk
Event:
GTC Silicon Valley
Year:
2015
Session ID:
S5579
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Abstract:
Learn about the best practice variant calling pipeline that drives every DNA sequencing project in the world be it for research, industry or to diagnose a patient in critical condition. Here we present the different approaches to optimize and accelerate key parts of this pipeline. First we will give you an overview of the process and how researchers around the world are using DNA sequencing data to understand complex and rare variants and their associations with disease. Second we will show you the work we have done to speed up this pipeline through use of GPUs and other technologies. Third we will discuss a new version of the pipeline that takes advantage of the optimizations to enable incremental analysis, that is, leveraging all historical data on every new sequencing project with minimal overhead. We close this presentation by discussing the many points that are still open for optimization and how the community can get involved.
Learn about the best practice variant calling pipeline that drives every DNA sequencing project in the world be it for research, industry or to diagnose a patient in critical condition. Here we present the different approaches to optimize and accelerate key parts of this pipeline. First we will give you an overview of the process and how researchers around the world are using DNA sequencing data to understand complex and rare variants and their associations with disease. Second we will show you the work we have done to speed up this pipeline through use of GPUs and other technologies. Third we will discuss a new version of the pipeline that takes advantage of the optimizations to enable incremental analysis, that is, leveraging all historical data on every new sequencing project with minimal overhead. We close this presentation by discussing the many points that are still open for optimization and how the community can get involved.  Back
 
Topics:
Genomics & Bioinformatics
Type:
Talk
Event:
GTC Silicon Valley
Year:
2014
Session ID:
S4679
Streaming:
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