Genomic Applications on Cray supercomputers: Next Generation Sequencing Workflow

Abstract—Recent progress in DNA sequencing technology has yielded a new class of devices that allow for the analysis of genetic material with unprecedented speed and efficiency. These advances, styled under the name Next-Generation Sequencing (NGS), increasingly shift the burden from chemistry done in a laboratory to a string manipulation problem, well suited to High-Performance Computing (HPC). By breaking up DNA into millions of small strands (20 to 1000 bases) and reading them in parallel, the rate at which genetic material can be acquired has increased by several orders of magnitude at the expense of a new distinction between raw and processed genetic data. The technology that generates raw genomic data is becoming increasingly fast and inexpensive when compared to the rate that this data can be analyzed. In general, assembling small reads into a useful form is done by either assembling individual reads (de novo) or mapping these pieces against a reference (mapping). In this paper, we present our experience with Ray, a parallel short-read de novo assembler code. We also present a configuration for an NGS workflow based on Sonexion storage and Cray supercomputers. Keywords—Next-generation sequencing; assembler; DNA; high-performance computing; parallel; genome I