Добірка наукової літератури з теми "Accurate Alignment of Short Reads"
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Статті в журналах з теми "Accurate Alignment of Short Reads"
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.
Повний текст джерелаKumar, 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.
Повний текст джерелаFlouri, 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.
Повний текст джерелаTeixeira, 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.
Повний текст джерелаEbler, 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.
Повний текст джерелаLi, 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.
Повний текст джерелаMAURER-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.
Повний текст джерелаGhoneimy, 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.
Повний текст джерелаProdanov, 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.
Повний текст джерелаTeng, 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.
Повний текст джерелаДисертації з теми "Accurate Alignment of Short Reads"
Shajii, Ariya. "Fast and accurate alignment of barcoded reads." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118040.
Повний текст джерелаCataloged 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.
Porter, Jacob Stuart. "Mapping Bisulfite-Treated Short DNA Reads." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/82870.
Повний текст джерелаPh. D.
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.
Повний текст джерелаTran, 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.
Повний текст джерелаPh. D.
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.
Повний текст джерела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.
Частини книг з теми "Accurate Alignment of Short Reads"
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.
Повний текст джерела"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.
Повний текст джерелаTait, 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.
Повний текст джерелаD. 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.
Повний текст джерелаТези доповідей конференцій з теми "Accurate Alignment of Short Reads"
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.
Повний текст джерелаCui, 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.
Повний текст джерелаBingol, 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.
Повний текст джерелаLu, 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.
Повний текст джерелаYang, 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.
Повний текст джерелаNickol, 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.
Повний текст джерелаFlory, 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.
Повний текст джерелаBu¨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.
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