Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning

The advent of new sequencing technology has generated massive amounts of biological data at unprecedented rates. High-throughput bioinformatics tools are required to keep pace with this. Here, we implement a workflow-based model for parallelizing the data intensive task of genome alignment and variant calling with BWA and GATK´s Haplotype Caller. We explore different approaches of partitioning data and how each affect the run time. We observe granularity-based partitioning for BWA and alignment-based partitioning for Halo type Caller to be the optimal choices for the pipeline. We identify the various challenges encountered while developing such an application and provide an insight into addressing them. We report significant performance improvements, from 12 days to 4 hours, while running the BWA-GATK pipeline using 100 nodes for analyzing high-coverage oak tree data.