BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.

INFORMATION VISUALIZATION TO SUPPORT MANAGEMENT DECISIONS

Information visualization can accelerate perception, provide insight and control, and harness this flood of valuable data to gain a competitive advantage in making business decisions. Although such a statement seems to be obvious, there is a lack in the literature of practical evidence of the benefit of information visualization. The main contribution of this paper is to illustrate how, for a major European apparel retailer, the visualization of performance information plays a critical role in improving business decisions and in extracting insights from Redio Frequency Idetification (RFID)-based performance measures. In this paper, we identify - based on a literature review - three fundamental managerial functions of information visualization, namely as: a communication medium, a knowledge management means, and a decision-support instrument. Then, we provide - based on real industrial case evidence - how information visualization supports business decision-making. Several examples are provided to evidence the benefit of information visualization through its three identified managerial functions. We find that - depending on the way performance information is shaped, communicated, and made interactive - it not only helps decision making, but also offers a means of knowledge creation, as well as an appropriate communication channel. © 2014 World Scientific Publishing Company.