Academic literature on the topic 'Accurate Alignment of Short Reads'
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Journal articles on the topic "Accurate Alignment of Short Reads"
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Asghari, Hossein, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, and Faraz Hach. "CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme." Bioinformatics 36, no. 12 (April 7, 2020): 3703–11. http://dx.doi.org/10.1093/bioinformatics/btaa232.
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Abstract Motivation The ubiquitous abundance of circular RNAs (circRNAs) has been revealed by performing high-throughput sequencing in a variety of eukaryotes. circRNAs are related to some diseases, such as cancer in which they act as oncogenes or tumor-suppressors and, therefore, have the potential to be used as biomarkers or therapeutic targets. Accurate and rapid detection of circRNAs from short reads remains computationally challenging. This is due to the fact that identifying chimeric reads, which is essential for finding back-splice junctions, is a complex process. The sensitivity of discovery methods, to a high degree, relies on the underlying mapper that is used for finding chimeric reads. Furthermore, all the available circRNA discovery pipelines are resource intensive. Results We introduce CircMiner, a novel stand-alone circRNA detection method that rapidly identifies and filters out linear RNA sequencing reads and detects back-splice junctions. CircMiner employs a rapid pseudo-alignment technique to identify linear reads that originate from transcripts, genes or the genome. CircMiner further processes the remaining reads to identify the back-splice junctions and detect circRNAs with single-nucleotide resolution. We evaluated the efficacy of CircMiner using simulated datasets generated from known back-splice junctions and showed that CircMiner has superior accuracy and speed compared to the existing circRNA detection tools. Additionally, on two RNase R treated cell line datasets, CircMiner was able to detect most of consistent, high confidence circRNAs compared to untreated samples of the same cell line. Availability and implementation CircMiner is implemented in C++ and is available online at https://github.com/vpc-ccg/circminer. Supplementary information Supplementary data are available at Bioinformatics online.
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Kumar, Sanjeev, Suneeta Agarwal, and Ranvijay. "Fast and memory efficient approach for mapping NGS reads to a reference genome." Journal of Bioinformatics and Computational Biology 17, no. 02 (April 2019): 1950008. http://dx.doi.org/10.1142/s0219720019500082.
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New generation sequencing machines: Illumina and Solexa can generate millions of short reads from a given genome sequence on a single run. Alignment of these reads to a reference genome is a core step in Next-generation sequencing data analysis such as genetic variation and genome re-sequencing etc. Therefore there is a need of a new approach, efficient with respect to memory as well as time to align these enormous reads with the reference genome. Existing techniques such as MAQ, Bowtie, BWA, BWBBLE, Subread, Kart, and Minimap2 require huge memory for whole reference genome indexing and reads alignment. Gapped alignment versions of these techniques are also 20–40% slower than their respective normal versions. In this paper, an efficient approach: WIT for reference genome indexing and reads alignment using Burrows–Wheeler Transform (BWT) and Wavelet Tree (WT) is proposed. Both exact and approximate alignments are possible by it. Experimental work shows that the proposed approach WIT performs the best in case of protein sequence indexing. For indexing, the reference genome space required by WIT is 0.6[Formula: see text]N (N is the size of reference genome) whereas existing techniques BWA, Subread, Kart, and Minimap2 require space in between 1.25[Formula: see text]N to 5[Formula: see text]N. Experimentally, it is also observed that even using such small index size alignment time of proposed approach is comparable in comparison to BWA, Subread, Kart, and Minimap2. Other alignment parameters accuracy and confidentiality are also experimentally shown to be better than Minimap2. The source code of the proposed approach WIT is available at http://www.algorithm-skg.com/wit/home.html .
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Flouri, Tomas, Costas S. Iliopoulos, Solon P. Pissis, and German Tischler. "Mapping Short Reads to a Genomic Sequence with Circular Structure." International Journal of Systems Biology and Biomedical Technologies 1, no. 1 (January 2012): 26–34. http://dx.doi.org/10.4018/ijsbbt.2012010103.
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Constant advances in DNA sequencing technologies are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data, in the form of short sequences (reads), need to be mapped back onto reference sequences, a few gigabases long. A first generation of short-read alignment algorithms successfully employed hash tables, and the current second generation uses the Burrows-Wheeler transform, further improving speed and memory footprint. These next-generation sequencing technologies allow researchers to characterise a bacterial genome, during a single experiment, at a moderate cost. In this article, as most of the bacterial chromosomes contain a circular DNA molecule, the authors present a new simple, yet efficient, sensitive and accurate algorithm, specifically designed for mapping millions of short reads to a genomic sequence with circular structure.
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Teixeira, Andreia Sofia, Francisco Fernandes, and Alexandre P. Francisco. "SpliceTAPyR — An Efficient Method for Transcriptome Alignment." International Journal of Foundations of Computer Science 29, no. 08 (December 2018): 1297–310. http://dx.doi.org/10.1142/s0129054118430049.
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RNA-Seq is a Next-Generation Sequencing (NGS) protocol for sequencing the messenger RNA in a cell and generates millions of short sequence fragments, reads, in a single run. These reads can be used to measure levels of gene expression and to identify novel splice variants of genes. One of the critical steps in an RNA-Seq experiment is mapping NGS reads to the reference genome. Because RNA-Seq reads can span over more than one exon in the genome, this task is challenging. In the last decade, tools for RNA-Seq alignment have emerged, but most of them run in two phases. First, the pipeline only maps reads that have a direct match in the reference, and the remaining are set aside as initially unmapped reads. Then, they use heuristics based approaches, clustering or even annotations, to decide where to align the later. This work presents an efficient computational solution for the problem of transcriptome alignment, named SpliceTAPyR. It identifies signals of splice junctions and relies on compressed full-text indexing methods and succinct data structures to efficiently align RNA-Seq reads in a single phase. This way it achieves the same or better accuracy than other tools while using considerably less memory and time to the most competitive tools.
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Ebler, Jana, Peter Ebert, Wayne E. Clarke, Tobias Rausch, Peter A. Audano, Torsten Houwaart, Yafei Mao, et al. "Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes." Nature Genetics 54, no. 4 (April 2022): 518–25. http://dx.doi.org/10.1038/s41588-022-01043-w.
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AbstractTypical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers. In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation—a process we refer to as genome inference. Compared with mapping-based approaches, PanGenie is more than 4 times faster at 30-fold coverage and achieves better genotype concordances for almost all variant types and coverages tested. Improvements are especially pronounced for large insertions (≥50 bp) and variants in repetitive regions, enabling the inclusion of these classes of variants in genome-wide association studies. PanGenie efficiently leverages the increasing amount of haplotype-resolved assemblies to unravel the functional impact of previously inaccessible variants while being faster compared with alignment-based workflows.
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Li, H., and R. Durbin. "Fast and accurate short read alignment with Burrows-Wheeler transform." Bioinformatics 25, no. 14 (May 18, 2009): 1754–60. http://dx.doi.org/10.1093/bioinformatics/btp324.
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MAURER-STROH, SEBASTIAN, VITHIAGARAN GUNALAN, WING-CHEONG WONG, and FRANK EISENHABER. "A SIMPLE SHORTCUT TO UNSUPERVISED ALIGNMENT-FREE PHYLOGENETIC GENOME GROUPINGS, EVEN FROM UNASSEMBLED SEQUENCING READS." Journal of Bioinformatics and Computational Biology 11, no. 06 (December 2013): 1343005. http://dx.doi.org/10.1142/s0219720013430051.
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We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with specific tag motifs. This approach was applied to the test case of fitting the enterohemorrhagic O104:H4 E.coli strain from the 2011 outbreak in Germany into the phylogenetic network of previously known E.coli-related strains and extend the method to allow assigning any new strain to the correct phylogenetic group even directly from unassembled short sequence reads from next generation sequencing data. Hence, this approach is also useful to quickly identify the most suitable reference genome for subsequent assembly steps.
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Ghoneimy, Samy, and Samir Abou El-Seoud. "A MapReduce Framework for DNA Sequencing Data Processing." International Journal of Recent Contributions from Engineering, Science & IT (iJES) 4, no. 4 (December 30, 2016): 11. http://dx.doi.org/10.3991/ijes.v4i4.6537.
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<p class="Els-1storder-head">Genomics and Next Generation Sequencers (NGS) like Illumina Hiseq produce data in the order of 200 billion base pairs in a single one-week run for a 60x human genome coverage, which requires modern high-throughput experimental technologies that can only be tackled with high performance computing (HPC) and specialized software algorithms called “short read aligners”. This paper focuses on the implementation of the DNA sequencing as a set of MapReduce programs that will accept a DNA data set as a FASTQ file and finally generate a VCF (variant call format) file, which has variants for a given DNA data set. In this paper MapReduce/Hadoop along with Burrows-Wheeler Aligner (BWA), Sequence Alignment/Map (SAM) tools, are fully utilized to provide various utilities for manipulating alignments, including sorting, merging, indexing, and generating alignments. The Map-Sort-Reduce process is designed to be suited for a Hadoop framework in which each cluster is a traditional N-node Hadoop cluster to utilize all of the Hadoop features like HDFS, program management and fault tolerance. The Map step performs multiple instances of the short read alignment algorithm (BoWTie) that run in parallel in Hadoop. The ordered list of the sequence reads are used as input tuples and the output tuples are the alignments of the short reads. In the Reduce step many parallel instances of the Short Oligonucleotide Analysis Package for SNP (SOAPsnp) algorithm run in the cluster. Input tuples are sorted alignments for a partition and the output tuples are SNP calls. Results are stored via HDFS, and then archived in SOAPsnp format. The proposed framework enables extremely fast discovering somatic mutations, inferring population genetical parameters, and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. It also demonstrate that this method achieves comparable accuracy to alternative methods for sequencing data processing.</p><p class="Abstract"><em></em><em><br /></em></p>
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Prodanov, Timofey, and Vikas Bansal. "Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications." Nucleic Acids Research 48, no. 19 (October 9, 2020): e114-e114. http://dx.doi.org/10.1093/nar/gkaa829.
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Abstract The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies. Although long-read sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies can potentially overcome this limitation, long segmental duplications with high sequence identity pose challenges for long-read mapping. We describe a probabilistic method, DuploMap, designed to improve the accuracy of long-read mapping in segmental duplications. It analyzes reads mapped to segmental duplications using existing long-read aligners and leverages paralogous sequence variants (PSVs)—sequence differences between paralogous sequences—to distinguish between multiple alignment locations. On simulated datasets, DuploMap increased the percentage of correctly mapped reads with high confidence for multiple long-read aligners including Minimap2 (74.3–90.6%) and BLASR (82.9–90.7%) while maintaining high precision. Across multiple whole-genome long-read datasets, DuploMap aligned an additional 8–21% of the reads in segmental duplications with high confidence relative to Minimap2. Using DuploMap-aligned PacBio circular consensus sequencing reads, an additional 8.9 Mb of DNA sequence was mappable, variant calling achieved a higher F1 score and 14 713 additional variants supported by linked-read data were identified. Finally, we demonstrate that a significant fraction of PSVs in segmental duplications overlaps with variants and adversely impacts short-read variant calling.
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Teng, Carolina, Renan Weege Achjian, Jiang Chau Wang, and Fernando Josepetti Fonseca. "Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance." Applied Sciences 13, no. 7 (March 30, 2023): 4385. http://dx.doi.org/10.3390/app13074385.
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In genomic analysis, long reads are an emerging type of data processed by assembly algorithms to recover the complete genome sample. They are, on average, one or two orders of magnitude longer than short reads from the previous generation, which provides important advantages in information quality. However, longer sequences bring new challenges to computer processing, undermining the performance of assembly algorithms developed for short reads. This issue is amplified by the exponential growth of genetic data generation and by the slowdown of transistor technology progress, illustrated by Moore’s Law. Minimap2 is the current state-of-the-art long-read assembler and takes dozens of CPU hours to assemble a human genome with clinical standard coverage. One of its bottlenecks, the alignment stage, has not been successfully accelerated on FPGAs in the literature. GACT-X is an alignment algorithm developed for FPGA implementation, suitable for any size input sequence. In this work, GACT-X was adapted to work as the aligner of Minimap2, and these are integrated and implemented in an FPGA cloud platform. The measurements for accuracy and speed-up are presented for three different datasets in different combinations of numbers of kernels and threads. The integrated solution’s performance limitations due to data transfer are also analyzed and discussed.
Dissertations / Theses on the topic "Accurate Alignment of Short Reads"
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Shajii, Ariya. "Fast and accurate alignment of barcoded reads." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118040.
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Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 57-62).
Over the last few years, we have seen the emergence of several so-called "third-generation" sequencing platforms, which improve on standard short-read sequencing that has thus far been at the center of next-generation sequencing. While technologies developed by Pacific Biosciences and Oxford Nanopore accomplish this goal by producing physically longer reads, several other technologies take an alternate route by instead producing "barcoded reads", including 10x Genomics' Chromium platform and Illumina's TruSeq Synthetic Long-Read platform. With barcoded reads, long-range information is captured by the barcodes, which identify source DNA fragments. As with all sequencing data, alignment of barcoded reads is the first step in nearly all analyses, and therefore plays a central role. Here, we design and validate improved alignment algorithms for barcoded sequencing data, which enable improved downstream analyses like phasing and genotyping, and additionally uncover variants in regions containing nearby homologous elements that go undetected by other methods.
by Ariya Shajii.
S.M.
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Porter, Jacob Stuart. "Mapping Bisulfite-Treated Short DNA Reads." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/82870.
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Epigenetics are stable heritable traits that are not a result of the DNA sequence. Epigenetic modification of DNA cytosine plays a role in development and disease. The covalent bonding of a methyl group or a hydroxymethyl group to the 5-carbon of cytosine epigenetically modifies cytosine to 5-methylcytosine or 5-hydroxymethylcytosine. Upon PCR amplification, the bisulfite treatment of DNA converts unmethylated cytosine to thymine, while 5-methylcytosine, 5-hydroxymethylcytosine, and other bases remain unchanged. The resulting sequences can be mapped to a reference genome; however, this can be challenging due to sequencing technology complexity, low sequence complexity, and biases and errors introduced with bisulfite treatment. Once the short read is mapped, the identity of 5-methylcytosine or 5-hydroxymethylcytosine can be determined by comparing the mapped read to the aligned reference genome. Bisulfite DNA read mapping is characterized by mapping performance as low as 40%. This research improves bisulfite short read mapping quality. First, reads generated from the bisulfite hairpin PCR protocol are used to study mapping failure and solutions. A read may not map to the genome; it may map uniquely, or it may map to multiple locations. Sequence complexity correlates with these mapping categories. The hairpin protocol allows for a recovery, in some cases, of the original untreated read, and mapping this read with the regular read mapper Bowtie2 improved mapper performance by 10%. New bisulfite read mapping software called BisPin was created that calls BFAST (BLAT-like Fast Accurate Search Tool) for mapping. BisPin resolves ambiguously mapped reads with a rescoring strategy, which yields a statistically significant improvement. BFAST-Gap for Ion Torrent reads was developed, since Ion Torrent machines are less expensive than Illumina machines and since Ion Torrent reads are longer. There are few mappers for Ion Torrent data. BFAST-Gap uses homopolymer run length for contextual gap penalty functions, since homopolymer runs cause errors in Ion Torrent reads. In conjunction with BisPin, this software performed well on real and simulated bisulfite Ion Torrent data and Illumina data. InfoTrim, a read trimmer with an entropy term, was developed with competitive results.Ph. D.
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Berger, Simon A. [Verfasser], and A. [Akademischer Betreuer] Stamatakis. "Phylogeny-Aware Placement and Alignment Methods for Short Reads / Simon A. Berger. Betreuer: A. Stamatakis." Karlsruhe : KIT-Bibliothek, 2013. http://d-nb.info/1032243139/34.
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Tran, Hong Thi Thanh. "Evaluating and Improving Performance of Bisulfite Short Reads Alignment and the Identification of Differentially Methylated Sites." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/81861.
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Large-scale bisulfite treatment and short reads sequencing technology allows comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. The thesis work first evaluates the performance of several commonly used bisulfite short read mappers and investigates how pre-processing data might affect the performance. Aligning bisulfite short reads to a reference genome remains a challenging task. In practice, only a limited proportion of bisulfite treated DNA reads can be mapped uniquely (around 50-70%) while a significant proportion of reads (called multireads) are aligned to multiple genomic locations. The thesis outlines a strategy to improve the mapping efficiencies of the existing bisulfite short reads software by finding unique locations for multireads. Analyses of both simulated data and real hairpin bisulfite sequencing data show that our strategy can effectively assign approximately 70% of the multireads to their best locations with up to 90% accuracy, leading to a significant increase in the overall mapping efficiency.
The most common and essential downstream task in DNA methylation analysis is to detect differential methylated cytosines (DMCs). Although many statistical methods have been applied to detect DMCs, inconsistency in detecting differential methylated sites among statistical tools remains. We adapt the wavelet-based functional mixed models (WFMM) to detect DMCs. Analyses of simulated Arabidopsis data show that WFMM has higher sensitivities and specificities in detecting DMCs compared to existing methods especially when methylation differences are small. Analyses of monozygotic twin data who have different pain sensitivity also show that WFMM can find more relevant DMCs related to pain sensitivity compared to methylKit. In addition, we provide a strategy to modify the default settings in both WFMM and methylKit to be more tailored to a given methylation profile, thus improving the accuracy of detecting DMCs.
Population growth and climate change leave billions of people around the world living in water scarcity conditions. Therefore, utility of reclaimed water (treated wastewater) is pivotal for water sustainability. Recently, researchers discovered microbial regrowth problems in reclaimed water distribution systems (RWDs). The third part of the thesis involves: 1) identifying fundamental conditions that affect proliferation of antibiotic resistance genes (ARGs), 2) identifying the effect of water chemistry and water age on microbial regrowth, and 3) characterizing co-occurrence of ARGs and/or mobile genetics elements (MGEs), i.e., plasmids in simulated RWDs. Analyses of preliminary results from simulated RWDs show that biofilms, bulk water environment, temperature, and disinfectant types have significant influence on shaping antibiotic resistant bacteria (ARB) communities. In particular, biofilms create a favorable environment for ARGs to diversify but with lower total ARG populations. ARGs are the least diverse at 300C and the most diverse at 220C. Disinfectants reduce ARG populations as well as ARG diversity. Chloramines keep ARG populations and diversity at the lowest rate. Disinfectants work better in bulk water environment than in biofilms in terms of shaping resistome. Network analysis on assembly data is done to determine which ARG pairs are the most co-occurred. Bayesian network is more consistent with the co-occurrence network constructed from assembly data than the network based on Spearman's correlation network of ARG abundance profiles.Ph. D.
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Lee, Sheng Ta, and 李昇達. "Develop RNA short reads alignment tool based on GPU with CUDA." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/22829209401562854641.
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碩士長庚大學
資訊工程學系
100
After the reference genomes of many organisms are sequenced in the post-genetic era, an important issue is to do the re-sequencing of individual genomes with high-throughput reads. Many next-generation sequencing machines have been proposed in the last few years and a series of re-sequencing tools have been developed for mapping short reads to the reference genome. FRESCO is a frequency-based re-sequencing tool without using hash look-up table algorithm and Burrows Wheeler Transformation. FRESCO offers more flexibility in the mapping and then obtains satisfied mapping results. However, FRESCO is a computation-intensive tool. Therefore, in this paper, a tool, CUDA-FRESCO , was proposed to reduce the computation time of FRESCO by using the graphics processing units with CUDA. By comparing to FRESCO, CUDA-FRESCO achieved 63x speedups for the mapping kernel and 20x speedups for the overall computation time. Further more, we discovered the bottleneck of massive data transfer with CUDA-FRESCO. Soon after we proposed the CUDA-FRESCO 2.0 to solve this problem; we compare with FRESCO on different GPUs, we can get 53x to 141x speedups for the overall computation time.
Book chapters on the topic "Accurate Alignment of Short Reads"
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CLEMENTE, JOSÉ C., JESPER JANSSON, and GABRIEL VALIENTE. "ACCURATE TAXONOMIC ASSIGNMENT OF SHORT PYROSEQUENCING READS." In Biocomputing 2010, 3–9. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789814295291_0002.
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"A Short Reads Alignment Algorithm Oriented to Massive Data." In Current Trends in Computer Science and Mechanical Automation Vol.1, 49–57. De Gruyter Open Poland, 2017. http://dx.doi.org/10.1515/9783110584974-008.
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Tait, Roger, and Gerald Schaefer. "Distributed Medical Volume Registration." In Handbook of Research on Distributed Medical Informatics and E-Health, 180–89. IGI Global, 2009. http://dx.doi.org/10.4018/978-1-60566-002-8.ch012.
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The registration of corresponding patient volumes is often a pre-requisite for medical imaging tasks. Accurate alignment, however, usually results in high computational complexity and can hence take a considerable amount of time. This is particularly true with 3-D volume data which adds another dimension to the registration process. One possibility of keeping registration times feasible is to distribute computation among several processors so that it maybe accomplished in parallel. This chapter provides a short survey of parallel registration approaches which have been proposed together with some recent research adopting a blackboard architecture for distributed high performance image and volume registration purposes.
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D. Magar, Nakul, Priya Shah, K. Harish, Tejas C. Bosamia, Kalyani M. Barbadikar, Yogesh M. Shukla, Amol Phule, et al. "Gene Expression and Transcriptome Sequencing: Basics, Analysis, Advances." In Gene Expression [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.105929.
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Gene expression studies are extremely useful for understanding a broad range of biological, physiological, and molecular responses. The techniques for gene expression reflect differential patterns of gene regulation and have evolved with time from detecting one gene to many genes at a time laterally. Gene expression depends on the spatiotemporal expression in a particular tissue at a given time point and needs critical examination and interpretation. Transcriptome sequencing or RNA-seq using next-generation sequencing (short and long reads) is the most widely deployed technology for accurate quantification of gene expression. According to the biological aim of the experiment, replications, platform, and chemistries, propelling improvement has been demonstrated and documented using RNA-seq in plants, humans, animals, and clinical sciences with respect to gene expression of mRNA, small non-coding, long non-coding RNAs, alternative splice variations, isoform variations, gene fusions, single-nucleotide variants. Integrating transcriptome sequencing with other techniques such as chromatin immunoprecipitation, methylation, genome-wide association studies, manifests insights into genetic and epigenetic regulation. Epi-transcriptome including RNA methylation, modification, and alternative polyadenylation events can also be explored through long-read sequencing. In this chapter, we have presented an account of the basics of gene expression methods, transcriptome sequencing, and the various methodologies involved in the downstream analysis.
Conference papers on the topic "Accurate Alignment of Short Reads"
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Natarajan, Santhi, N. Krishna Kumar, Debnath Pal, and S. K. Nandy. "AccuRA: Accurate alignment of short reads on scalable reconfigurable accelerators." In 2016 International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS). IEEE, 2016. http://dx.doi.org/10.1109/samos.2016.7818334.
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Cui, Xingchen, Hongzhi Shi, Jian Zhao, Yuan Ge, Yunfeng Yin, and Kun Zhao. "High Accuracy Short Reads Alignment Using Multiple Hash Index Tables on FPGA Platform." In 2020 IEEE 5th Information Technology and Mechatronics Engineering Conference (ITOEC). IEEE, 2020. http://dx.doi.org/10.1109/itoec49072.2020.9141738.
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Bingol, Zulal, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, and Can Alkan. "GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping." In 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2021. http://dx.doi.org/10.1109/ipdpsw52791.2021.00039.
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Lu, Zhi-Yuan, Jian-Ming Xie, and Xiao Sun. "Umap: Use Unique Sequence for Alignment of Short Sequence Reads and SNP Detection." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5516449.
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Yang, Yongjie, Cheng Zhong, and Danyang Chen. "Accelerating Alignment for Short Reads Allowing Insertion of Gaps on Multi-Core Cluster." In 2019 20th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT). IEEE, 2019. http://dx.doi.org/10.1109/pdcat46702.2019.00019.
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Nickol, Jeremy B., Randall M. Mathison, Michael G. Dunn, Jong S. Liu, and Malak F. Malak. "Unsteady Heat Transfer and Pressure Measurements on the Airfoils of a Rotating Transonic Turbine With Multiple Cooling Configurations." In ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/gt2016-57768.
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Measurements are presented for a high-pressure transonic turbine stage operating at design-corrected conditions with forward and aft purge flow and blade film cooling in a short-duration blow-down facility. Four different film-cooling configurations are investigated: simple cylindrical-shaped holes, diffusing fan-shaped holes, an advanced-shaped hole, and uncooled blades. A rainbow turbine approach is used so each of the four blade types comprise a wedge of the overall bladed disk and are investigated simultaneously at identical speed and vane exit conditions. Double-sided Kapton heat-flux gauges are installed at midspan on all three film-cooled blade types, and single-sided Pyrex heat-flux gauges are installed on the uncooled blades. Kulite pressure transducers are installed at midspan on cooled blades with round and fan-shaped cooling holes. Experimental results are presented both as time-averaged values and as time-accurate encoder-averages. In addition, the results of a steady RANS CFD computation are compared to the time-averaged data. The computational and experimental results show that the cooled blades reduce heat transfer into the blade significantly from the uncooled case, but the overall differences in heat transfer among the three cooling configurations is small. This challenges previous conclusions for simplified geometries that show shaped cooling holes outperforming cylindrical holes by a great margin. It suggests that the more complicated flow physics associated with an airfoil operating in an engine-representative environment reduces the effectiveness of the shaped cooling holes. The experimental results appear to show a small benefit to the advanced cooling holes, but this is on the order of the variation caused by changes in the alignment of heat-flux gauges with cooling holes.
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Flory, Alan P., and William C. Livoti. "The Effect and Remedy of Nozzle Loads on Boiler Feed Pumps." In ASME 2004 Power Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/power2004-52157.
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Many frequently encountered start-up and operational problems in current design combined cycle power plants can be traced to pipe strain and nozzle loads placed upon pumps. This is most dramatic when the boiler feed pump is affected. Many of the symptoms are significant and can include misalignment, dynamic (changing) alignment, pump or motor vibration, bearing problems, mechanical seal failures and seizure of equipment on start-up and shutdown. While these are all nuisance items that can plague plant shake-down and commissioning, some can generate huge costs and plant unscheduled outages. More profoundly, these symptoms are often all present, making accurate diagnosis of the true cause very difficult. The real cost of these problems can be seen in plants missing commercial operation dates. Some of the piping issues that can cause these symptoms will be discussed, items including hydraulic aspects of the piping design, straight runs, horizontal runs, venting, location of minimum flow valve, and pipe hanger location. Also, the use of pre-fabricated pipe and spool pieces will be discussed. A short discussion will also be presented on how these piping issues impact various designs of pumps, such as barrel pumps, horizontal split case and ring section type pumps. This will also include some comments on pump mounting issues such as base-plate installation, the use of pin & key blocks and pedestal design. All of the discussions will be summarized and then presented with several recommendations for piping repair, operational changes, and material reinforcement. Optional pump features will be presented, indicating what items can be used to improve operation and reliability when abnormal nozzle loads are expected, including comments on internal clearances, wear part metallurgy and bearing upgrades. These recommendations will be compared against several field experiences for confirmation, with some focus on nozzle load data vs. design, and operation prior to and after strain removal. This combination of field results and engineering analysis of this topic should prove quite useful to the engineer attempting to diagnose any symptoms found in the field. Often times several symptoms may be present, making diagnosis difficult and it is only the methodical steps of symptom elimination that will get the new power plant on the way to commercial operation.
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Bu¨ttner, Lars, and Ju¨rgen Czarske. "Multimode Laser Doppler Anemometer for Turbulence Measurements With High Spatial Resolution." In ASME/JSME 2003 4th Joint Fluids Summer Engineering Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/fedsm2003-45598.
Full textAbstract:
The advantageous employment of multimode fibres for beam delivery in laser Doppler anemometers (LDA) is presented. Turbulent boundary layers can be investigated with high precision and high spatial resolution. For measurements of turbulence data usually hot wire anemometers are employed which, however, do not fulfil the requirement of non-intrusiveness. Therefore laser Doppler anemometers are employed which are limited by the size of their measurement volume of usually about 50 μm × 100 mm. The spatial resolution can be improved by a stronger focusing or by using a side receiver, which restricts the detection area. Furthermore, the measurement of turbulence data is limited by the varying fringe spacing, which pretends a non-existing degree of turbulence (“virtual turbulence”) and is caused by the wave-front curvature of the employed Gaussian laser mode. In this contribution it is demonstrated, that the employment of multimode-light with beam quality factors M2 >> 1 the length of the measurement volume is reduced to a few percent compared to the intersection volume length of the two laser beams because of the low spatial coherence of the multimode light. The uniformity of the fringe spacing is significantly improved. The variation of fringe spacing (“virtual turbulence”) is less than 0.05%. The multimode-fibre LDA (MMF-LDA) combines the advantages of both a short measurement volume guaranteeing a high spatial resolution as well as low virtual turbulence in one device. It is therefore well suited for high accurate determination of velocity gradients in laminar or turbulent boundary layers. A MMF-LDA with about 100 fringes and 5·10−4 fringe spacing variation within a measurement volume of length 80 μm was used to perform fluid measurements in a wind tunnel. The remaining turbulence intensity of the free wind tunnel stream was determined to 0.3%. Boundary layer measurements on a well-known laminar velocity profile, the Blasius boundary layer, were performed and the wall shear stress was determined. All results are in excellent agreement with the theory. Measurements of turbulent boundary layers are presented. Multimode fibres allow the transfer of significantly higher power into the LDA measurement volume and need lower alignment effort compared to the usually employed single-mode fibres. Powerful laser diodes can now be applied for LDA set-ups, enabling sensitive velocity measurements of fluid flows.