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. This technology is referred as Next-Generation Sequencing ( NGS). It produces large quantities of small fragments of DNA, called reads. 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).However, the success of the new technology to generate data faster has come at a price. Sequencers will produce reads that are too small (< 150 base pairs (bp)) for overlap-layout consensus assemblers. These advances increasingly shift the burden from chemistry done in a laboratory to a string manipulation problem, well suited to High-Performance Computing (HPC). This technology has also shifted the traditional paradigm in computational chemistry from looking at single applications to optimizing an entire workflow. 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 presentation, we review what is involved in NGS workflows from an HPC point of view and how traditional computational chemists need to look at the workflow from a holistic point of view. We also emphasize recent work optimizing de novo assemblers to leverage HPC as we move closer toward personalized medicine.

Traditional computational chemistry expanding into a new dimension: Big data

248th National Meeting (2014)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.