GPU-Accelerated BWT Construction for Large Collection of Short Reads

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many state-of-the-art aligners, at their core, have used the Burrows-Wheeler transform (BWT) as a main-memory index of a reference genome (typical example, NCBI human genome). Recently, BWT has also found its use in string-graph assembly, for indexing the reads (i.e., raw data from DNA sequencers). In a typical data set, the volume of reads is tens of times of the sequenced genome and can be up to 100 Gigabases. Note that a reference genome is relatively stable and computing the index is not a frequent task. For reads, the index has to computed from scratch for each given input. The ability of efficient BWT construction becomes a much bigger concern than before. In this paper, we present a practical method called CX1 for constructing the BWT of very large string collections. CX1 is the first tool that can take advantage of the parallelism given by a graphics processing unit (GPU, a relative cheap device providing a thousand or more primitive cores), as well as simultaneously the parallelism from a multi-core CPU and more interestingly, from a cluster of GPU-enabled nodes. Using CX1, the BWT of a short-read collection of up to 100 Gigabases can be constructed in less than 2 hours using a machine equipped with a quad-core CPU and a GPU, or in about 43 minutes using a cluster with 4 such machines (the speedup is almost linear after excluding the first 16 minutes for loading the reads from the hard disk). The previously fastest tool BRC is measured to take 12 hours to process 100 Gigabases on one machine; it is non-trivial how BRC can be parallelized to take advantage a cluster of machines, let alone GPUs.Comment: 11 page

Microstructural stability and lattice misfit characterization of nimonic 263

Nimonic 263 has been selected as a candidate header/piping material of advanced ultra-supercritical (A-USC) boilers for the next generation of fossil fuel power plant. Experimental assessments on the microstructural stability of this material are presented in this paper. Microstructural evolution has been quantified by high resolution field emission SEM and TEM. Electron diffraction and the combined XRD and Gaussian peak-fitting have been applied to investigate the coherency and lattice misfit between the gamma prime precipitates and the gamma matrix. The microstructure subjected to solution and hardening treatment consists of gamma-matrix and a network of carbide precipitates along the grain boundaries. Large quantities of fine gamma prime-Ni3(Ti,Al) precipitates were observed, with an average size of 17 nm and coherent with the matrix lattice. The overall misfit has been quantified to be 0.28%. After long term aging at 700 and 725 °C for various periods up to 20,000 hours, gamma prime was still the predominant precipitate and mostly coherent with the matrix. A few needle-shape eta-Ni3Ti intermetallic precipitates were found in the grain boundary regions. The gamma prime size has grown progressively to 78 nm, accompanied by the gamma-gamma prime constrained misfit increasing to 0.50%. Moreover, the M23C6-type grain boundary carbides were found to have experienced morphological evolution, including the nucleation of Widmanstatten-type needles and their initial growth towards the matrix

A conceptual plan for the Detroit Book and Tower Building: Exploration of the conjunction of historic preservation and sustainable design concepts

This conceptual project generated an adaptive reuse proposal for the Book and Tower Building in a registered historic district. Louis Kamper designed the thirteen-story Book Building in 1917, in the Beaux Arts style, to create elite shops and offices. In 1926 the thirty-six-story Tower Building extended the leaseable space. This proposal preserved and rehabilitated the historic features in the lobby area and renovated the retail spaces. An Asian Café was designed to contrast, but blend with, the Beaux Arts style. The Secretary of the Interior’s Standards for Rehabilitation were followed in the lobby area so as to make the renovation eligible for federal and state tax credits. LEED for New Construction & Major Renovation Criteria grounded the proposal so as to reduce the potentially negative environmental impact associated with renovation of urban high-rise buildings. The contrast of new and old, East and West, created an intriguing tension in this Detroit landmark

Singing voice correction using canonical time warping

Expressive singing voice correction is an appealing but challenging problem. A robust time-warping algorithm which synchronizes two singing recordings can provide a promising solution. We thereby propose to address the problem by canonical time warping (CTW) which aligns amateur singing recordings to professional ones. A new pitch contour is generated given the alignment information, and a pitch-corrected singing is synthesized back through the vocoder. The objective evaluation shows that CTW is robust against pitch-shifting and time-stretching effects, and the subjective test demonstrates that CTW prevails the other methods including DTW and the commercial auto-tuning software. Finally, we demonstrate the applicability of the proposed method in a practical, real-world scenario

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and without a GPU, respectively. MEGAHIT assembles the data as a whole, i.e., it avoids pre-processing like partitioning and normalization, which might compromise on result integrity. MEGAHIT generates 3 times larger assembly, with longer contig N50 and average contig length than the previous assembly. 55.8% of the reads were aligned to the assembly, which is 4 times higher than the previous. The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license.Comment: 2 pages, 2 tables, 1 figure, submitted to Oxford Bioinformatics as an Application Not

Improving QCD with fermions: the 2 dimensional case of QCD with Sea Quarks

We study QCD in 2 dimensions using the improved lattice fermionic Hamiltonian proposed by Luo, Chen, Xu and Jiang. The vector mass and the chiral condensate are computed for various $SU(N_C)$ gauge groups. We do observe considerable improvement in comparison with the Wilson quark case.Comment: LATTICE98(improvement