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Relevant bibliographies by topics / Read mapping

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Academic literature on the topic 'Read mapping'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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Journal articles on the topic "Read mapping"

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Chon, Alvin, and Xiaoqiu Huang. "SRAMM: Short Read Alignment Mapping Metrics." International Journal on Bioinformatics & Biosciences 11, no. 02 (2021): 01–07. http://dx.doi.org/10.5121/ijbb.2021.11201.

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Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods generally are neither standardized nor well described in literature or software manuals. Additionally, third party mapping quality programs are typically computationally intensive or designed for specific applications. SRAMM efficiently generates multiple different concept-based mapping scores to provide for an informative post alignment examination and filtering

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Tran, Hong, Jacob Porter, Ming-an Sun, Hehuang Xie, and Liqing Zhang. "Objective and Comprehensive Evaluation of Bisulfite Short Read Mapping Tools." Advances in Bioinformatics 2014 (April 15, 2014): 1–11. http://dx.doi.org/10.1155/2014/472045.

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Background. Large-scale bisulfite treatment and short reads sequencing technology allow 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. Aligning bisulfite short reads to a reference genome has been a challenging task. We compared five bisulfite short read mapping tools, BSMAP, Bismark, BS-Seeker, BiSS, and BRAT-BW, representing two classes of mapping alg

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Canzar, Stefan, and Steven L. Salzberg. "Short Read Mapping: An Algorithmic Tour." Proceedings of the IEEE 105, no. 3 (2017): 436–58. http://dx.doi.org/10.1109/jproc.2015.2455551.

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Kaufmann, Jodi. "Mapping Territories." International Review of Qualitative Research 1, no. 3 (2008): 347–59. http://dx.doi.org/10.1525/irqr.2008.1.3.347.

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Space is gendered. Not only is it constructed along a male/female binary (Duncan, 1996), it also emerges within a transgender dimension. Beyond the work of Nameste (2000) on space and who has the right to occupy it and Haberstam (2005) on space and the archive, there is a paucity of literature discussing transsexual space. Yet, learning to read this space is important, for it is within space that transsexual bodies are conscribed to the margins, erased in explosive passion, and allowed to become human (Butler, 2004). Although one can read space in different ways (Agnew, 2005), one does not cho

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Hovhannisyan, Hrant, Ahmed Hafez, Carlos Llorens, and Toni Gabaldón. "CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies." Bioinformatics 36, no. 3 (2019): 925–27. http://dx.doi.org/10.1093/bioinformatics/btz626.

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Abstract Motivation Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library

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Edgar, Robert. "URMAP, an ultra-fast read mapper." PeerJ 8 (June 24, 2020): e9338. http://dx.doi.org/10.7717/peerj.9338.

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Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB re

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Southgate, Joel A., Matthew J. Bull, Clare M. Brown, et al. "Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications." Bioinformatics 36, no. 6 (2019): 1681–88. http://dx.doi.org/10.1093/bioinformatics/btz814.

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Abstract Motivation Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results Standard human reference viruses were insufficient for mappin

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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 (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 a

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Jaroszyński, Piotr, and Norbert Dojer. "Efficient and Error-Tolerant Sequencing Read Mapping." Current Bioinformatics 10, no. 2 (2015): 191–98. http://dx.doi.org/10.2174/157489361002150518125716.

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Kim, Jongik, Chen Li, and Xiaohui Xie. "Improving read mapping using additional prefix grams." BMC Bioinformatics 15, no. 1 (2014): 42. http://dx.doi.org/10.1186/1471-2105-15-42.

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Dissertations / Theses on the topic "Read mapping"

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Chacon, de San Baldomero Alejandro. "Read mapping on heterogeneous systems: scalability strategies for bioinformatic primitives." Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/671736.

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La seqüenciació genòmica és un component clau en nous avenços en medicina, i la seva democratització és un pas important per millorar l’accessibilitat per al pacient. Els beneficis implícits en el descobriment de noves variants genètiques són molt amplis, incloent des de la detecció precoç de càncer com la medicina personalitzada, passant pel disseny de fàrmacs i l’edició genòmica. Tots aquests usos potencials han incrementat exponencialment l’interès de la comunitat científica en el camp de la bioinformàtica durant els últims anys. A més, el sorgiment dels mètodes de Seqüenciació de Nova Gen

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Hoffmann, Steve. "Genome Informatics for High-Throughput Sequencing Data Analysis." Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-152643.

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This thesis introduces three different algorithmical and statistical strategies for the analysis of high-throughput sequencing data. First, we introduce a heuristic method based on enhanced suffix arrays to map short sequences to larger reference genomes. The algorithm builds on the idea of an error-tolerant traversal of the suffix array for the reference genome in conjunction with the concept of matching statistics introduced by Chang and a bitvector based alignment algorithm proposed by Myers. The algorithm supports paired-end and mate-pair alignments and the implementation offers methods fo

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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

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Emde, Anne-Katrin [Verfasser]. "Next-generation sequencing algorithms : from read mapping to variant detection / Anne-Katrin Emde." Berlin : Freie Universität Berlin, 2013. http://d-nb.info/1045194964/34.

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Otto, Christian. "The mapping task and its various applications in next-generation sequencing." Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-161623.

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The aim of this thesis is the development and benchmarking of computational methods for the analysis of high-throughput data from tiling arrays and next-generation sequencing. Tiling arrays have been a mainstay of genome-wide transcriptomics, e.g., in the identification of functional elements in the human genome. Due to limitations of existing methods for the data analysis of this data, a novel statistical approach is presented that identifies expressed segments as significant differences from the background distribution and thus avoids dataset-specific parameters. This method detects differen

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Long, Evan Michael. "Genomic Structural Variation Across Five Continental Populations of Drosophila melanogaster." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7335.

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Chromosomal structure variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismalphenotype. Some of these effects are caused by structural variations containing genes. Modern sequencing using short reads makes the detection of large structural variations (> 1kb) very difficult. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of Drosophila melanogaster (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent

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Schena, Jucinara. "Mapping press’s political ideology: a content analysis of editorial articles from the most read Brazilian online newspapers." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/670418.

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Aware of the well-studied non-neutrality of media and the challenge that represents to have mechanisms to objectively identify the ideological bias, this thesis provides a methodological proposal to assess the political ideology of newspapers. The model’s originality lies on merging the contribution from political and communication sciences, as it is built considering the core values of political ideologies. The model is qualitatively inspired by the Critical Discourse Analysis perspective, and quantitatively by the traditional Content Analysis. It allows to compare samples according to an ide

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Hilker, Rolf [Verfasser]. "Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains / Rolf Hilker." Bielefeld : Universitätsbibliothek Bielefeld, 2015. http://d-nb.info/108012991X/34.

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Brinda, Karel. "Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit." Thesis, Paris Est, 2016. http://www.theses.fr/2016PESC1027/document.

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Depuis leur émergence autour de 2006, les technologies de séquençage haut débit ont révolutionné la recherche biologique et médicale. Obtenir instantanément une grande quantité de courtes ou longues lectures de presque tout échantillon biologique permet de détecter des variantes génomiques, révéler la composition en espèces d’un métagénome, déchiffrer la biologie du cancer, décoder l'évolution d’espèces vivantes ou disparues, ou mieux comprendre les schémas de la migration humaine et l'histoire humaine en général. La vitesse à laquelle augmente le débit des technologies de séquençage dépasse l

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Fujimoto, Masaki Stanley. "Graph-Based Whole Genome Phylogenomics." BYU ScholarsArchive, 2020. https://scholarsarchive.byu.edu/etd/8461.

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Understanding others is a deeply human urge basic in our existential quest. It requires knowing where someone has come from and where they sit amongst peers. Phylogenetic analysis and genome wide association studies seek to tell us where we’ve come from and where we are relative to one another through evolutionary history and genetic makeup. Current methods do not address the computational complexity caused by new forms of genomic data, namely long-read DNA sequencing and increased abundances of assembled genomes, that are becoming evermore abundant. To address this, we explore specialized dat

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Books on the topic "Read mapping"

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Wilmott, Clancy. Mobile Mapping. Amsterdam University Press, 2020. http://dx.doi.org/10.5117/9789462984530.

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This book argues for a theory of mobile mapping, a situated and spatial approach towards researching how everyday digital mobile media practices are bound up in global systems of knowledge and power. Drawing from literature in media studies and geography -- and the work of Michel Foucault and Doreen Massey -- it examines how geographical and historical material, social, and cultural conditions are embedded in the way in which contemporary (digital) cartographies are read, deployed, and engaged. This is explored through seventeen walking interviews in Hong Kong and Sydney, as potent discourses

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Torres, Luis A. Real-Time Mapping alert system: User's manual. U.S. Geological Survey, 1996.

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Torres, Luis A. Real-Time Mapping alert system: User's manual. U.S. Geological Survey, 1996.

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Torres, Luis A. Real-Time Mapping alert system: Characteristics and capabilities. U.S. Geological Survey, 1995.

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Graczyk, Jacek. The real Fatou conjecture. Princeton University Press, 1998.

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North Carolina. Land Records Management Program. Technical specifications for base, cadastral, and digital mapping. The Program, 1987.

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Baouendi, M. Salah. Real submanifolds in complex space and their mappings. Princeton University Press, 1999.

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Elizabeth, Baigent, ed. The cadastral map in the service of the state: A history of property mapping. University of Chicago Press, 1992.

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Preston, Christopher J. Iterates of piecewise monotone mappings on an interval. Universität Bielefeld, Schwerpunkt Mathematisierung, 1987.

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Preston, Christopher J. Iterates of piecewise monotone mappings on an interval. Springer-Verlag, 1988.

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Book chapters on the topic "Read mapping"

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Ribeca, Paolo. "Short-Read Mapping." In Bioinformatics for High Throughput Sequencing. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4614-0782-9_7.

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Zhou, Xueya, Suying Bao, Binbin Wang, Xuegong Zhang, and You-Qiang Song. "Short Read Mapping for Exome Sequencing." In Methods in Molecular Biology. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-514-9_6.

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Menzel, Peter, Jes Frellsen, Mireya Plass, Simon H. Rasmussen, and Anders Krogh. "On the Accuracy of Short Read Mapping." In Methods in Molecular Biology. Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-514-9_3.

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Morshedi, Mostafa, and Hamid Noori. "FPGA Implementation of a Short Read Mapping Accelerator." In Lecture Notes in Computer Science. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-56258-2_25.

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Mäkinen, Veli, Niko Välimäki, Antti Laaksonen, and Riku Katainen. "Unified View of Backward Backtracking in Short Read Mapping." In Algorithms and Applications. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12476-1_13.

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Wang, Zhanyong, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, and Eleazar Eskin. "CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29627-7_34.

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Yang, Ye, and Juan Liu. "JVM: Java Visual Mapping Tool for Next Generation Sequencing Read." In Advances in Experimental Medicine and Biology. Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-017-9245-5_2.

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Melnyk, Viktor, and Ivan Lopit. "Optimization of Read-Only Memory Program Models Mapping into the FPGA Architecture." In Advances in Intelligent Systems and Computing. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-46586-9_3.

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Kimura, Kouichi, Asako Koike, and Kenta Nakai. "Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-23038-7_14.

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Gainza, Mariana de. "Materialist Variations on Spinoza." In Materialism and Politics. ICI Berlin Press, 2021. http://dx.doi.org/10.37050/ci-20_01.

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Common assertions suppose an incompatibility between critical-dialectical philosophies and Spinozist political ontologies, and allow for an Adornian critique of Spinoza’sEthics: to live in accordance with one’s own being is a form of compliance to dominant values. By mapping contemporary Spinozism I show that within its tensions there is a place for dialectics, one which can be read in dialogue with the Adornian gesture denouncing the purported identity between particular and universal.

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Conference papers on the topic "Read mapping"

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Dai, Dong, Xi Li, Chao Wang, and Xuehai Zhou. "Cloud Based Short Read Mapping Service." In 2012 IEEE International Conference on Cluster Computing (CLUSTER). IEEE, 2012. http://dx.doi.org/10.1109/cluster.2012.60.

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Olson, Corey B., Maria Kim, Cooper Clauson, et al. "Hardware Acceleration of Short Read Mapping." In 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2012. http://dx.doi.org/10.1109/fccm.2012.36.

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Arram, James, Kuen Hung Tsoi, Wayne Luk, and Peiyong Jiang. "Reconfigurable Acceleration of Short Read Mapping." In 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2013. http://dx.doi.org/10.1109/fccm.2013.57.

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Chen, Yupeng, Bertil Schmidt, and Douglas L. Maksell. "An FPGA aligner for short read mapping." In 2012 22nd International Conference on Field Programmable Logic and Applications (FPL). IEEE, 2012. http://dx.doi.org/10.1109/fpl.2012.6339267.

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"ACCURATE LONG READ MAPPING USING ENHANCED SUFFIX ARRAYS." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003126201020107.

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Knodel, Oliver, Thomas B. Preusser, and Rainer G. Spallek. "Next-generation massively parallel short-read mapping on FPGAs." In 2011 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP). IEEE, 2011. http://dx.doi.org/10.1109/asap.2011.6043268.

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Duan, Xiaohui, Kai Xu, Yuandong Chan, et al. "S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light." In 2017 IEEE International Conference on Cluster Computing (CLUSTER). IEEE, 2017. http://dx.doi.org/10.1109/cluster.2017.16.

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Chen, Yupeng, Bertil Schmidt, and Douglas Leslie Maskell. "Accelerating short read mapping on an FPGA (abstract only)." In the ACM/SIGDA international symposium. ACM Press, 2012. http://dx.doi.org/10.1145/2145694.2145740.

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Preuber, Thomas B., Oliver Knodel, and Rainer G. Spallek. "Short-Read Mapping by a Systolic Custom FPGA Computation." In 2012 IEEE 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM). IEEE, 2012. http://dx.doi.org/10.1109/fccm.2012.37.

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Aji, Ashwin M., Liqing Zhang, and Wu-chun Feng. "GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors." In 2010 IEEE 13th International Conference on Computational Science and Engineering (CSE). IEEE, 2010. http://dx.doi.org/10.1109/cse.2010.29.

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Reports on the topic "Read mapping"

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Cohen, Jonathan, Christ Tchou, Tim Hawkins, and Paul Debevec. Real-Time High-Dynamic Range Texture Mapping. Defense Technical Information Center, 2001. http://dx.doi.org/10.21236/ada459538.

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Tang, Dezheng. Mapping Programs to Parallel Architectures in the Real World. Portland State University Library, 2000. http://dx.doi.org/10.15760/etd.6418.

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Salerno, Mario. Mapping Between Nonlinear Schrödinger Equations with Real and Complex Potentials. Jgsp, 2013. http://dx.doi.org/10.7546/jgsp-32-2013-25-35.

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Christie, Benjamin, Osama Ennasr, and Garry Glaspell. Autonomous navigation and mapping in a simulated environment. Engineer Research and Development Center (U.S.), 2021. http://dx.doi.org/10.21079/11681/42006.

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Unknown Environment Exploration (UEE) with an Unmanned Ground Vehicle (UGV) is extremely challenging. This report investigates a frontier exploration approach, in simulation, that leverages Simultaneous Localization And Mapping (SLAM) to efficiently explore unknown areas by finding navigable routes. The solution utilizes a diverse sensor payload that includes wheel encoders, three-dimensional (3-D) LIDAR, and Red, Green, Blue and Depth (RGBD) cameras. The main goal of this effort is to leverage frontier-based exploration with a UGV to produce a 3-D map (up to 10 cm resolution). The solution pr

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Schmidt, Henrik, and John Leonard. GOATS'2002, Multi-AUV Cooperative Behavior for Littoral MCM and REA Concurrent Mapping and Localization. Defense Technical Information Center, 2002. http://dx.doi.org/10.21236/ada629097.

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Kaltenbacher, Eric, David Costello, and Kendall Carder. Compact Optical Imager for Real-time, 3-D Range, Intensity and Fluorescence Mapping of the Ocean Floor. Defense Technical Information Center, 2006. http://dx.doi.org/10.21236/ada612266.

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Kaltenbacher, Eric, James Patten, David Costello, and Kendall Carder. Compact Optical Imager for Real-time, 3-D Range, Intensity and Fluorescence Mapping of the Ocean Floor. Defense Technical Information Center, 2003. http://dx.doi.org/10.21236/ada629485.

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Siddiqui, A., D. Romascanu, E. Golovinsky, and M. Rahman,Y. Transport Mappings for Real-time Application Quality-of-Service Monitoring (RAQMON) Protocol Data Unit (PDU). RFC Editor, 2006. http://dx.doi.org/10.17487/rfc4712.

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IIT RESEARCH INST LANHAM MD. Mapping of the Embedded Real-Time Trusted Computer Systems (ERT-TCSs) Requirements into the Trusted Computer System Evaluation Criteria. Defense Technical Information Center, 1990. http://dx.doi.org/10.21236/ada241207.

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