San Francisco
June 30 - July 2, 2014

Spark Summit 2014 brought the Apache Spark community together on June 30- July 2, 2014 at the The Westin St. Francis in San Francisco. It featured production users of Spark, Shark, Spark Streaming and related projects.


Spark Summit 2014
ADAM: Fast, Scalable Genomic Analysis
Frank Austin Nothaft (UC Berkeley)

ADAM is a high-performance distributed processing pipeline and API for DNA sequencing data. To allow computation to scale on clusters with more than a hundred nodes, ADAM uses Apache Spark as a computational engine and stores data using Apache Avro and the open-source Parquet columnar store. This scalability allows us to perform complex, computationally heavy tasks such as base quality score recalibration (BQSR), or duplicate marking on high coverage human genomes (> 60%, 236GB) in under a half hour. In tests on the Amazon Elastic Compute platform, we achieve a 50% speedup over current processing pipelines, and a lower processing cost.
To achieve scalability in a distributed setting, we rephrased conventional sequential DNA processing algorithms as data-parallel algorithms. In this talk, we’ll discuss the general principles we used for making these algorithms scalable while achieving full concordance with the equivalent serial algorithms. Additionally, by adapting genomic analysis to a commodity distributed analytics platform like Apache Spark, it is easier to perform ad hoc analysis and machine learning on genomic data. We will discuss how this impacts the clinical use of DNA analysis pipelines, as well as population genomics.

Frank Austin Nothaft is a graduate student in the AMP and ASPIRE labs at UC-Berkeley, and is advised by Prof. David Patterson. His current focus is on high performance computer systems for bioinformatics, and is involved in the ADAM, avocado, and FireBox projects. Prior to Berkeley, Frank worked at Broadcom in Irvine, CA on high performance electronic design automation. Frank has a Bachelors of Science with Honors in Electrical Engineering from Stanford University.

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