To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60%. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1% FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.

Abstract. We consider online scheduling algorithms in the dynamic speed scaling model, where a processor can scale its speed between 0 and some maximum speed T . The processor uses energy at rate s α when run at speed s, where α > 1 is a constant. Most modern processors use dynamic speed scaling to manage their energy usage. This leads to the problem of designing execution strategies that are both energy efficient, and yet have almost optimum performance. We consider two problems in this model and give essentially optimum possible algorithms for them. In the first problem, jobs with arbitrary sizes and deadlines arrive online and the goal is to maximize the throughput, i.e. the total size of jobs completed successfully. We give an algorithm that is 4-competitive for throughput and O(1)-competitive for the energy used. This improves upon the 14 throughput competitive algorithm of Chan et al. [10]. Our throughput guarantee is optimal as any online algorithm must be at least 4-competitive even if the energy concern is ignored [7]. In the second problem, we consider optimizing the trade-off between the total flow time incurred and the energy consumed by the jobs. We give a 4-competitive algorithm to minimize total flow time plus energy for unweighted unit size jobs, and a (2 + o(1))α/ ln α-competitive algorithm to minimize fractional weighted flow time plus energy. Prior to our work, these guarantees were known only when the processor speed was unbounded (T = ∞) [4].

No abstract

Abstract. We study online scheduling to minimize flow time plus energy usage in the dynamic speed scaling model. We devise new speed scaling functions that depend on the number of active jobs, replacing the existing speed scaling functions in the literature that depend on the remaining work of active jobs. The new speed functions are more stable and also more efficient. They can support better job selection strategies to improve the competitive ratios of existing algorithms [5,8], and, more importantly, to remove the requirement of extra speed. These functions further distinguish themselves from others as they can readily be used in the non-clairvoyant model (where the size of a job is only known when the job finishes). As a first step, we study the scheduling of batched jobs (i.e., jobs with the same release time) in the non-clairvoyant model and present the first competitive algorithm for minimizing flow time plus energy (as well as for weighted flow time plus energy); the performance is close to optimal.