Genomics researchers today are faced with an ever-increasing amount of data to analyze, and yet they have a difficult time leveraging modern frameworks and technologies (like Spark and cloud infrastructure) to efficiently and accurately analyze their data. This practical guide provides the guidance these researchers need. With this book, you’ll learn how to combine algorithms designed for genomics with the leading tool for big data—Spark—and the ascendant paradigm of working in the cloud with Docker.
Dr. Brian O’Connor is the Technical Director of the UCSC Genomics Institute Analysis Core. There he focuses on the development and deployment of large-scale, cloud-based systems for analyzing genomics data. This includes the Toil workflow execution platform, which is designed to run genomic pipelines on a wide range of cloud environments including AWS, Azure, Google and OpenStack, and ADAM, a distributed genomics platform developed in collaboration with UC Berkeley. He is also the co-chair of the Containers and Workflows task team of the Global Alliance for Genomics and Health (GA4GH) where he works on tool and workflow container standards. Brian recently joined UCSC from the Ontario Institute for Cancer Research (OICR) where his previous projects included leading the technical implementation of cloud-based analysis systems for the PanCancer Analysis of Whole Genomes (PCAWG) effort, the creation of the Dockstore project (http://dockstore.org), and the development of the International Cancer Genome Consortium’s Data Portal (http://dcc.icgc.org).
Geraldine Van der Auwera is the Benevolent Dictator For Life of the GATK user community. As such she is in charge of GATK documentation, tech support and keeping user riots down to a minimum. She joined the Broad Institute in 2012 after earning a PhD in Microbial Genomics from the University of Louvain-la-Neuve in Belgium then surviving a 4-year postdoctoral stint at Harvard Medical School, leaving behind the bench and pipette work forever.
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