The rapid development of high-throughput sequencing technologies means that hundreds of gigabytes of sequencing data can be produced in a single study. Many bioinformatics tools require counts of substrings of length k in DNA/RNA sequencing reads obtained for applications such as genome and transcriptome assembly, error correction, multiple sequence alignment, and repeat detection. Recently, several techniques have been developed to count k-mers in large sequencing datasets, with a trade-off between the time and memory required to perform this function. We assessed several k-mer counting programs and evaluated their relative performance, primarily on the basis of runtime and memory usage. We also considered additional parameters such as disk usage, accuracy, parallelism, the impact of compressed input, performance in terms of counting large k values and the scalability of the application to larger datasets.We make specific recommendations for the setup of a current state-of-the-art program and suggestions for further development.

Background: In bioinformatics, estimation of k-mer abundance histograms or just enumerating the number of unique k-mers and the number of singletons are desirable in many genome sequence analysis applications. The applications include predicting genome sizes, data pre-processing for de Bruijn graph assembly methods (tune runtime parameters for analysis tools), repeat detection, sequencing coverage estimation, measuring sequencing error rates, etc. Different methods for cardinality estimation in sequencing data have been developed in recent years. Objective: In this article, we present a comparative assessment of the different k-mer frequency estimation programs (ntCard, KmerGenie, KmerStream and Khmer (abundance-dist-single.py and unique-kmers.py) to assess their relative merits and demerits. Methods: Principally, the miscounts/error-rates of these tools are analyzed by rigorous experimental analysis for a varied range of k. We also present experimental results on runtime, scalability for larger datasets, memory, CPU utilization as well as parallelism of k-mer frequency estimation methods. Results: The results indicate that ntCard is more accurate in estimating F0, f1 and full k-mer abundance histograms compared with other methods. ntCard is the fastest but it has more memory requirements compared to KmerGenie. Conclusion: The results of this evaluation may serve as a roadmap to potential users and practitioners of streaming algorithms for estimating k-mer coverage frequencies, to assist them in identifying an appropriate method. Such results analysis also help researchers to discover remaining open research questions, effective combinations of existing techniques and possible avenues for future research.

No abstract

Parallelization of the finite-element method (FEM) has been contemplated by the scientific and high-performance computing community for over a decade. Most of the computations in the FEM are related to linear algebra that includes matrix and vector computations. These operations have the single-instruction multiple-data (SIMD) computation pattern, which is beneficial for shared-memory parallel architectures. General-purpose graphics processing units (GPGPUs) have been effectively utilized for the parallelization of FEM computations ever since 2007. The solver step of the FEM is often carried out using conjugate gradient (CG)type iterative methods because of their larger convergence rates and greater opportunities for parallelization. Although the SIMD computation patterns in the FEM are intrinsic for GPU computing, there are some pitfalls, such as the underutilization of threads, uncoalesced memory access, lower arithmetic intensity, limited faster memories on GPUs and synchronizations. Nevertheless, FEM applications have been successfully deployed on GPUs over the last 10 years to achieve a significant performance improvement. This paper presents a comprehensive review of the parallel optimization strategies applied in each step of the FEM. The pitfalls and tradeoffs linked to each step in the FEM are also discussed in this paper. Furthermore, some extraordinary methods that exploit the tremendous amount of computing power of a GPU are also discussed. The proposed review is not limited to a single field of engineering. Rather, it is applicable to all fields of engineering and science in which FEM-based simulations are necessary.

Abstract-This paper presents a comparison of OpenMP andOpenCL based on the parallel implementation of algorithms from various fields of computer applications. The focus of our study is on the performance of benchmark comparing OpenMP and OpenCL. We observed that OpenCL programming model is a good option for mapping threads on different processing cores. Balancing all available cores and allocating sufficient amount of work among all computing units, can lead to improved performance. In our simulation, we used Fedora operating system; a system with Intel Xeon Dual core processor having thread count 24 coupled with NVIDIA Quadro FX 3800 as graphical processing unit.