The human reference genome serves as the foundation for genomics by providing a scaffold for alignment of sequencing reads, but currently only reflects a single consensus haplotype, which impairs read alignment and downstream analysis accuracy. Reference genome structures incorporating known genetic variation have been shown to improve the accuracy of genomic analyses, but have so far remained computationally prohibitive for routine large-scale use. Here we present a graph genome implementation that enables read alignment across 2,800 diploid genomes encompassing 12.6 million SNPs and 4.0 million indels. Our Graph Genome Pipeline requires 6.5 hours to process a 30x coverage WGS sample on a system with 36 CPU cores compared with 11 hours required by the GATK Best Practices pipeline.Using complementary benchmarking experiments based on real and simulated data, we show that using a graph genome reference improves read mapping sensitivity and produces a 0.5% increase in variant calling recall, or about 20,000 additional variants being detected per sample, while variant calling specificity is unaffected. Structural variations (SVs) incorporated into a graph genome can be genotyped accurately under a unified framework. Finally, we show that iterative augmentation of graph genomes yields incremental gains in variant calling accuracy. Our implementation is a significant advance towards fulfilling the promise of graph genomes to radically enhance the scalability and accuracy of genomic analyses.
The human reference genome serves as the foundation for genomics by providing a scaffold for alignment of sequencing reads, but currently only reflects a single consensus haplotype, which impairs read alignment and downstream analysis accuracy. Reference genome structures incorporating known genetic variation have been shown to improve the accuracy of genomic analyses, but have so far remained computationally prohibitive for routine large-scale use. Here we present a graph genome implementation that enables read alignment across 2,800 diploid genomes encompassing 12.6 million SNPs and 4.0 million indels. Our Graph Genome Pipeline requires 6.5 hours to process a 30x coverage WGS sample on a system with 36 CPU cores compared with 11 hours required by the GATK Best Practices pipeline.
In this correspondence, we propose a novel, efficient, and effective Refined Histogram (RH) for modeling the wavelet subband detail coefficients and present a new image signature based on the RH model for supervised texture classification. Our RH makes use of a step function with exponentially increasing intervals to model the histogram of detail coefficients, and the concatenation of the RH model parameters for all wavelet subbands forms the so-called RH signature. To justify the usefulness of the RH signature, we discuss and investigate some of its statistical properties. These properties would clarify the sufficiency of the signature to characterize the wavelet subband information. In addition, we shall also present an efficient RH signature extraction algorithm based on the coefficient-counting technique, which helps to speed up the overall classification system performance. We apply the RH signature to texture classification using the well-known databases. Experimental results show that our proposed RH signature in conjunction with the use of symmetrized Kullback-Leibler divergence gives a satisfactory classification performance compared with the current state-of-the-art methods.
Containers are an emerging technology that hold promise for improving productivity and code portability in scientific computing. We examine Linux container technology for the distribution of a non-trivial scientific computing software stack and its execution on a spectrum of platforms from laptop computers through to high performance computing (HPC) systems. We show on a workstation and a leadership-class HPC system that when deployed appropriately there are no performance penalties running scientific programs inside containers. For Python code run on large parallel computers, the run time is reduced inside a container due to faster library imports. The software distribution approach and data that we present will help developers and users decide on whether container technology is appropriate for them. We also provide guidance for the vendors of HPC systems that rely on proprietary libraries for performance on what they can do to make containers work seamlessly and without performance penalty.
Abstract. The scalar and vector Laplacians are basic operators in physics and engineering. In applications, they frequently show up perturbed by lowerorder terms. The effect of such perturbations on mixed finite element methods in the scalar case is well-understood, but that in the vector case is not. In this paper, we first show that, surprisingly, for certain elements there is degradation of the convergence rates with certain lower-order terms even when both the solution and the data are smooth. We then give a systematic analysis of lower-order terms in mixed methods by extending the Finite Element Exterior Calculus (FEEC) framework, which contains the scalar, vector Laplacian, and many other elliptic operators as special cases. We prove that stable mixed discretization remains stable with lower-order terms for sufficiently fine discretization. Moreover, we derive sharp improved error estimates for each individual variable. In particular, this yields new results for the vector Laplacian problem which are useful in applications such as electromagnetism and acoustics modeling. Further our results imply many previous results for the scalar problem and thus unifies them all under the FEEC framework.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.