Relevant bibliographies by topics / Short Read Mapping (SRM)

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'Short Read Mapping (SRM)'

Author: Grafiati
Published: 6 September 2023
Last updated: 31 July 2025

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Journal articles on the topic "Short Read Mapping (SRM)"

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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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Cline, Eliot, Nuttachat Wisittipanit, Tossapon Boongoen, Ekachai Chukeatirote, Darush Struss, and Anant Eungwanichayapant. "Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data." PeerJ 8 (December 7, 2020): e10501. http://dx.doi.org/10.7717/peerj.10501.

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Background Low-coverage sequencing is a cost-effective way to obtain reads spanning an entire genome. However, read depth at each locus is low, making sequencing error difficult to separate from actual variation. Prior to variant calling, sequencer reads are aligned to a reference genome, with alignments stored in Sequence Alignment/Map (SAM) files. Each alignment has a mapping quality (MAPQ) score indicating the probability a read is incorrectly aligned. This study investigated the recalibration of probability estimates used to compute MAPQ scores for improving variant calling performance in
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Yang, Xiaohong, Yue Li, Yu Wei, Zhanlong Chen, and Peng Xie. "Water Body Extraction from Sentinel-3 Image with Multiscale Spatiotemporal Super-Resolution Mapping." Water 12, no. 9 (2020): 2605. http://dx.doi.org/10.3390/w12092605.

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Water body mapping is significant for water resource management. In the view of 21 spectral bands and a short revisit time of no more than two days, a Sentinel-3 OLCI (Ocean and Land Colour Instrument) image could be the optimum data source in the near-real-time mapping of water bodies. However, the image is often limited by its low spatial resolution in practice. Super-resolution mapping (SRM) is a good solution to generate finer spatial resolution maps than the input data allows. In this paper, a multiscale spatiotemporal super-resolution mapping (MSST_SRM) method for water bodies is propose
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Alvin, Chon. "SRAMM: SHORT READ ALIGNMENT MAPPING METRICS." International Journal on Bioinformatics & Biosciences (IJBB) Vol 11, No.1/2, June 2021 11, June (2021): 1–7. https://doi.org/10.5281/zenodo.5084755.

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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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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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Deorowicz, Sebastian, and Adam Gudyś. "Whisper 2: Indel-sensitive short read mapping." SoftwareX 14 (June 2021): 100692. http://dx.doi.org/10.1016/j.softx.2021.100692.

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David, Matei, Misko Dzamba, Dan Lister, Lucian Ilie, and Michael Brudno. "SHRiMP2: Sensitive yet Practical Short Read Mapping." Bioinformatics 27, no. 7 (2011): 1011–12. http://dx.doi.org/10.1093/bioinformatics/btr046.

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Smith, A. D., W. Y. Chung, E. Hodges, et al. "Updates to the RMAP short-read mapping software." Bioinformatics 25, no. 21 (2009): 2841–42. http://dx.doi.org/10.1093/bioinformatics/btp533.

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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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Gao, Lei, Cong Wu, and Lin Liu. "AUSPP: A universal short-read pre-processing package." Journal of Bioinformatics and Computational Biology 17, no. 06 (2019): 1950037. http://dx.doi.org/10.1142/s0219720019500379.

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There are many short-read aligners that can map short reads to a reference genome/sequence, and most of them can directly accept a FASTQ file as the input query file. However, the raw data usually need to be pre-processed. Few software programs specialize in pre-processing raw data generated by a variety of next-generation sequencing (NGS) technologies. Here, we present AUSPP, a Perl script-based pipeline for pre-processing and automatic mapping of NGS short reads. This pipeline encompasses quality control, adaptor trimming, collapsing of reads, structural RNA removal, length selection, read m
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Dissertations / Theses on the topic "Short Read Mapping (SRM)"

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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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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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Natarajan, Santhi. "Accelerated and Accurate Alignment of Short Reads in High Throughput Next Generation Sequencing [NGS] Platforms." Thesis, 2016. http://etd.iisc.ac.in/handle/2005/4073.

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The genome of an organism encompasses the unique set of genetic instructions for every individual in a species. The genome, in totality, guides the course of evolution, development, genetic and epigenetic growth factors of an individual. Genomics, the study of genome, presents an interdisciplinary landscape, with a multistage data analytics pipeline. Understanding the genome involves determining the order of the four constituent nucleotides or bases or genetic alphabets, namely adenine (A), cytosine (C), guanine (G) and thymine (T), within the genome’s DNA sequence, and the process is widely k
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Book chapters on the topic "Short Read Mapping (SRM)"

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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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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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Fox, Heather A. "Mapping Spatial Consciousness in Kate Chopin’S Bayou Folk (1894)." In Arranging Stories. University Press of Mississippi, 2022. http://dx.doi.org/10.14325/mississippi/9781496840516.003.0002.

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This chapter traces the textual history of four stories—“Beyond the Bayou,” “The Return of Alcibiade,” “A Wizard from Gettysburg,” and “Ma’ame Pélagie”—from their initial publications in periodicals to their inclusion in Kate Chopin’s first short story collection, Bayou Folk (1894). These stories portray the aftermath of the Civil War in Louisiana between the 1860s and 1890s. When read together, they demonstrate a progressively deteriorating landscape, strategically revising northern magazine editors’ positioning of the South as sentimental and exotic to magnify the social concerns that contin
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Bhatia, Dinesh, and Animesh Mishra. "A Novel Artificial Intelligence Technique for Analysis of Real-Time Electro-Cardiogram Signal for the Prediction of Early Cardiac Ailment Onset." In Handbook of Research on Advancements of Artificial Intelligence in Healthcare Engineering. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-2120-5.ch003.

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The role of ECG analysis in the diagnosis of cardio-vascular ailments has been significant in recent times. Although effective, the present computational algorithms lack accuracy, and no technique till date is capable of predicting the onset of a CVD condition with precision. In this chapter, the authors attempt to formulate a novel mapping technique based on feature extraction using fractional Fourier transform (FrFT) and map generation using self-organizing maps (SOM). FrFT feature extraction from the ECG data has been performed in a manner reminiscent of short time Fourier transform (STFT).
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J. Espona, Maria. "Interdisciplinary Integrated Tools to Problem Solving 2.0." In Contemporary Issues in Information Systems - A Global Perspective. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.101456.

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Everyone understands the events they witness or read about according to their mental models, and that is one of the main reasons there are a lot of disagreements at workplaces and between friends and families. Considering this situation, plus the difficulty that most people face when trying to conceptualize problems, I suggest a course that includes series methodologies, working synergistically to deal with this problem that goes from understanding the differences between people to test multiple hypotheses and planning the solution implementation. Since 2014, I have been teaching with some col
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Fiore, Teresa. "All at One Point: The Unlikely Connections between Italy’s Emigration, Immigration, and (Post)Colonialism." In Pre-Occupied Spaces. Fordham University Press, 2017. http://dx.doi.org/10.5422/fordham/9780823274321.003.0001.

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The introduction opens with a reading of Italo Calvino’s poignant short story “All at One Point.” It relies on statistical data, sociological studies, and historical facts to address the connections between emigration from Italy and immigration to Italy, as well as Italian colonialism in Africa and the Mediterranean, and its postcolonial legacy. This intersection prompts a re-mapping of the Italian nation and poses Italy as a unique laboratory to rethink national belonging at large in our era of massive demographic mobility. The introduction explains the application of theories of space by de
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Conference papers on the topic "Short Read Mapping (SRM)"

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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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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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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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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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Sogabe, Yoko, and Tsutomu Maruyama. "An acceleration method of short read mapping using FPGA." In 2013 International Conference on Field-Programmable Technology (FPT). IEEE, 2013. http://dx.doi.org/10.1109/fpt.2013.6718385.

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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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Ng, Ho-Cheung, Izaak Coleman, Shuanglong Liu, and Wayne Luk. "Reconfigurable Acceleration of Short Read Mapping with Biological Consideration." In FPGA '21: The 2021 ACM/SIGDA International Symposium on Field Programmable Gate Arrays. ACM, 2021. http://dx.doi.org/10.1145/3431920.3439280.

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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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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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Reports on the topic "Short Read Mapping (SRM)"

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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule se
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Lunn, Pete, Marek Bohacek, Jason Somerville, Áine Ní Choisdealbha, and Féidhlim McGowan. PRICE Lab: An Investigation of Consumers’ Capabilities with Complex Products. ESRI, 2016. https://doi.org/10.26504/bkmnext306.

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Executive Summary This report describes a series of experiments carried out by PRICE Lab, a research programme at the Economic and Social Research Institute (ESRI) jointly funded by the Central Bank of Ireland, the Commission for Energy Regulation, the Competition and Consumer Protection Commission and the Commission for Communications Regulation. The experiments were conducted with samples of Irish consumers aged 18-70 years and were designed to answer the following general research question: At what point do products become too complex for consumers to choose accurately between the good ones
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