ADAM: Fast, Scalable Genomic Analysis

Download Slides

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.

« back
About Frank Austin Nothaft

Frank is the Technical Director for the Healthcare and Life Sciences vertical at Databricks. Prior to joining Databricks, Frank was a lead developer on the Big Data Genomics/ADAM and Toil projects at UC Berkeley, and worked at Broadcom Corporation on design automation techniques for industrial scale wireless communication chips. Frank holds a PhD and Masters of Science in Computer Science from UC Berkeley, and a Bachelor’s of Science with Honors in Electrical Engineering from Stanford University.