A survey of sequence alignment algorithms for next-generation sequencing

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Items 201–300 of 876

1. Speeding Up Large-Scale Next Generation Sequencing Data Analysis with pBWA
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2. Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine
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3. FANTOM: Functional and taxonomic analysis of metagenomes
   Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen · 2013 · BMC Bioinformatics
4. Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance
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5. Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects
   Rhys A. Farrer, Daniel A. Henk, Dan MacLean, David John Studholme, Matthew C. Fisher · 2013 · Scientific Reports
6. The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome
   Levent Albayrak, Kamil Khanipov, Maria Pimenova, George Golovko, Mark Rojas, Ioannis T. Pavlidis, Sergei Chumakov, Gerardo Aguilar, Arturo Chávez, William R. Widger et al. · 2016 · BMC Genomics
7. Accelerating Long Read Alignment on Three Processors
   Zonghao Feng, Shuang Qiu, Lipeng Wang, Qiong Luo · 2019 · Proceedings of the International Conference on Parallel Processing
8. Seed-and-vote based in-memory accelerator for DNA read mapping
   Ann Franchesca Laguna, Hasindu Gamaarachchi, Xunzhao Yin, Michael Thaddeus Niemier, Sri Parameswaran, Xiaobo Sharon Hu · 2020
9. Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform
   José Salavert Torres, I. B. Espert, A. T. Dominguez, V. Hernendez Garcia, Ignacio Medina Castello, J. Terraga Gimenez, Joaquı́n Dopazo · 2012 · IEEE Transactions on Computational Biology and Bioinformatics
10. Coverage‐based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
    Sarwar Azam, Vivek Thakur, Pradeep Ruperao, Trushar M. Shah, Jayashree Balaji, BhanuPrakash Amindala, Andrew D Farmer, David John Studholme, Gregory D. May, David Edwards et al. · 2012 · American Journal of Botany
11. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine
    Hao Ye, Joe Meehan, Weida Tong, Huixiao Hong · 2015 · Pharmaceutics
12. Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)
    Walther Parson, Christina Strobl, Gabriela E. Huber, Bettina Zimmermann, Sibylle M. Gomes, Luís Souto, Liane Fendt, Rhena Delport, Reina Langit, Sharon Wootton et al. · 2013 · Forensic Science International Genetics
13. Implementation of next generation sequencing in clinical molecular diagnostic laboratories: advantages, challenges and potential
    Rajesh R. Singh, Rajyalakshmi Luthra, Mark J. Routbort, Keyur Pravinchandra Patel, Leonard Jeffrey Medeiros · 2016 · Expert Review of Precision Medicine and Drug Development
14. Accurate high throughput alignment via line sweep-based seed processing
    Markus R. Schmidt, Klaus Heese, Arne Kutzner · 2019 · Nature Communications
15. Characterizing Multi-omic Data in Systems Biology
    Christopher E. Mason, Sandra G. Porter, T. M. F. Smith · 2013 · Advances in experimental medicine and biology
16. Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges
    Katherine Bruder, Kema Maiki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhan C. Watkins, Catherine Putonti · 2016 · Evolutionary Bioinformatics
17. A comparison of seed-and-extend techniques in modern DNA read alignment algorithms
    Nauman Ahmed, Koen Bertels, Zaid Al-Ars · 2016 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
18. Data Management Challenges in Next Generation Sequencing
    Sebastian Wandelt, Astrid Rheinländer, Marc Bux, Lisa Thalheim, Berit Haldemann, Ulf Leser · 2012 · Datenbank-Spektrum
19. Mutation Hot Spots in Yeast Caused by Long-Range Clustering of Homopolymeric Sequences
    Xin Ma, Maria V. Rogacheva, Koodali T Nishant, Sarah E. Zanders, Carlos D. Bustamante, Eric Alani · 2012 · Cell Reports
20. Α Quantum Pattern Recognition Method for Improving Pairwise Sequence Alignment
    Prousalis, Konstantinos, Konofaos, Nikos · 2019 · Scientific Reports
21. Benchmarking variant identification tools for plant diversity discovery
    Xing Wu, Christopher Heffelfinger, Hongyu Zhao, Stephen L. Dellaporta · 2019 · BMC Genomics
22. LVMapper: A Large-Variance Clone Detector Using Sequencing Alignment Approach
    Ming Wu, Pengcheng Wang, Kangqi Yin, Haoyu Cheng, Yun Xu, Chanchal Kumar Roy · 2020 · IEEE Access
23. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers
    Gina A. Garzón-Martínez, Jaime A. Osorio-Guarín, Paola Delgadillo-Durán, Franklin Mayorga, Felix E. Enciso-Rodríguez, David Landsman, Leonardo Mariño‐Ramírez, Luz Stella Barrero · 2015 · Plant Gene
24. BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
    Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier · 2018 · BMC Bioinformatics
25. Accelerating BWA-MEM Read Mapping on GPUs
    Minh Pham, Yi-Cheng Tu, Xiaoyi Lv · 2023 · International Conference on Supercomputing
26. FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions
    Alberto Gatto, Carlos Torroja, Francesco Mazzarotto, Stuart A. Cook, Paul J.R. Barton, Fátima Sánchez‐Cabo, Enrique Lara‐Pezzi · 2014 · Nucleic Acids Research
27. Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
    Johannes Köster, Louis Dijkstra, Tobias Marschall, Alexander Schönhuth · 2020 · Genome biology
28. Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study
    Matthew Parks, David Martin Lambert · 2015 · BMC Genomics
29. Whole exome sequencing is an efficient, sensitive and specific method of mutation detection in osteogenesis imperfecta and Marfan syndrome
    Aideen M McInerney-Leo, Mhairi S. Marshall, Brooke Gardiner, Paul J. Coucke, Lut Van Laer, Bart Loeys, KIM M. SUMMERS, Sofie Symoens, Jennifer A. West, Malcolm West et al. · 2013 · BoneKEy Reports
30. Discovery and characterization of Alu repeat sequences via precise local read assembly
    Julia V. Halo, Alayna Baron, Nicolette M Diroff, Jeffrey M. Kidd · 2015 · Nucleic Acids Research
31. Data-Driven Approaches in Antimicrobial Resistance: Machine Learning Solutions
    Aikaterini Sakagianni, Christina Koufopoulou, Petros Koufopoulos, Sofia Kalantzi, Nikolaos Theodorakis, Maria Nikolaou, Evgenia Paxinou, Dimitris Kalles, Vassilios S. Verykios, Pavlos M. Myrianthefs et al. · 2024 · Antibiotics
32. Methyl-CpG-Binding Domain Sequencing: MBD-seq
    Karolina A. Åberg, Robin F. Chan, Linying Xie, Andrey A. Shabalin, Edwin J. C. G. van den Oord · 2017 · Methods in molecular biology
33. Sequence graph transform (SGT): a feature embedding function for sequence data mining
    Chitta Ranjan, Samaneh Ebrahimi, Kamran Paynabar · 2022 · Data Mining and Knowledge Discovery
34. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
    Min-Te Chou, Bo Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, Jui‐Hung Hung · 2015 · Nucleic Acids Research
35. Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox
    Tongtong Zhang, Shengjun Tan, Na Tang, Yuanqing Li, Chenze Zhang, Jing Sun, Yanyan Guo, Hui Gao, Yujia Cai, Wen Hua Sun et al. · 2024 · Cell
36. Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing
    Melanie Febrer, Kirsten McLay, Mario Cáccamo, Kate B. Twomey, Robert Patrick Ryan · 2011 · Trends in biotechnology
37. Building a Genome Analysis Pipeline to Predict Disease Risk and Prevent Disease
    Yana Bromberg · 2013 · Journal of Molecular Biology
38. Integrating Epigenomics into the Understanding of Biomedical Insight
    Yixing Han, Ximiao He · 2016 · Bioinformatics and Biology Insights
39. Combining user behavioural information at the feature level to enhance continuous authentication systems
    Alejandro G. Martín, Isaac Martín de Diego, Alberto Fernández-Isabel, Marta Beltrán, Rubén R. Fernández · 2022 · Knowledge-Based Systems
40. Using VAAST to Identify Disease‐Associated Variants in Next‐Generation Sequencing Data
    Brett Kennedy, Zev N. Kronenberg, Hao Hu, Barry Moore, Steven D. Flygare, Martin G. Reese, Lynn B. Jorde, Mark D. Yandell, Chad Daniel Huff · 2014 · Current Protocols in Human Genetics
41. Highly sensitive and ultrafast read mapping for RNA-seq analysis
    Ignacio Medina, Joaquín Tárraga, Hèctor Martínez, Sergio Barrachina, Maribel Castillo, Justin E. Paschall, José Salavert Torres, Ignacio Blanquer-Espert, V. Hernández-García, Enrique S. Quintana–Ort́ı et al. · 2016 · DNA Research
42. Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
    Miriam Payá‐Milans, James W. Olmstead, Gerardo H. Nunez, Timothy A. Rinehart, Margaret E. Staton · 2018 · GigaScience
43. Approximate string matching using a bidirectional index
    Grégory Kucherov, Kamil Salikhov, Dekel Tsur · 2015 · Theoretical Computer Science
44. Stream as You Go: The Case for Incremental Data Access and Processing in the Cloud
    Romeo Kienzler, Rémy Bruggmann, Anand Ranganathan, Nesime Tatbul · 2012 · IEEE International Conference on Data Engineering Workshops (ICDEW)
45. Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species
    Tuan Viet Nguyen, Hyungtaek Jung, Guiomar Rotllant, David A. Hurwood, Peter Barclay Mather, Tomer Ventura · 2018 · Hydrobiologia
46. Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods
    Bartosz Ulaszewski, Joanna Meger, Jarosław Burczyk · 2021 · Forests
47. Plant MicroRNA Prediction by Supervised Machine Learning Using C5.0 Decision Trees
    Philip H. Williams, Rodney P. Eyles, Georg F. Weiller · 2012 · Journal of Nucleic Acids
48. Quantum gate algorithm for reference-guided DNA sequence alignment
    Georgios D. Varsamis, Ioannis G. Karafyllidis, K.M. Gilkes, U. Arranz, R. Martin-Cuevas, G. Calleja, Panagiotis Dimitrakis, Petros Kolovos, Raphael Sandaltzopoulos, H. C. Jessen et al. · 2023 · Computational Biology and Chemistry
49. Impact of RNA-seq attributes on false positive rates in differential expression analysis of de novo assembled transcriptomes
    Emmanuel González, Simon Joly · 2013 · BMC Research Notes
50. Characterization of NIST human mitochondrial DNA SRM-2392 and SRM-2392-I standard reference materials by next generation sequencing
    Sarah Riman, Kevin M. Kiesler, Lisa A. Borsuk, Peter M. Vallone · 2017 · Forensic Science International Genetics
51. Fast and memory efficient approach for mapping NGS reads to a reference genome
    Sanjeev Kumar, Suneeta Agarwal, Ranvijay · 2019 · Journal of Bioinformatics and Computational Biology
52. Approximate Two-Party Privacy-Preserving String Matching with Linear Complexity
    Martin Beck, Florian Kerschbaum · 2013 · IEEE International Congress on Big Data (BigData Congress)
53. PIM-Assembler: A Processing-in-Memory Platform for Genome Assembly
    Shaahin Angizi, Naima Ahmed Fahmi, Wei Zhang, Deliang Fan · 2020 · ACM/IEEE Design Automation Conference (DAC)
54. SNP Discovery Through Next-Generation Sequencing and Its Applications
    Santosh D. Kumar, Travis W. Banks, Sylvie Cloutier · 2016 · CRC Press eBooks
55. Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives
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56. A Review on Sequence Alignment Algorithms for Short Reads Based on Next-Generation Sequencing
    Jeongkyu Kim, Mingeun Ji, Gangman Yi · 2020 · IEEE Access
57. MemPool: A Scalable Manycore Architecture With a Low-Latency Shared L1 Memory
    Samuel Riedel, Matheus Cavalcante, Renzo Andri, Luca Benini C · 2023 · IEEE Transactions on Computers
58. A Survey of Copy‐Number Variation Detection Tools Based on High‐Throughput Sequencing Data
    Ruibin Xi, Semin Lee, Peter J. Park · 2012 · Current Protocols in Human Genetics
59. Determining the quality and complexity of next-generation sequencing data without a reference genome
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60. Additive methods for genomic signatures
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61. DART: a fast and accurate RNA-seq mapper with a partitioning strategy
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62. PIM-Aligner: A Processing-in-MRAM Platform for Biological Sequence Alignment
    Shaahin Angizi, Jiao Sun, Wei Zhang, Deliang Fan · 2020 · Design, Automation, and Test in Europe
63. Recent developments in genomics, bioinformatics and drug discovery to combat emerging drug-resistant tuberculosis
    Soumya Swaminathan, Jagadish Chandrabose Sundaramurthi, Alangudi Natarajan Palaniappan, Sujatha Narayanan · 2016 · Tuberculosis
64. Accelerating next generation sequencing data analysis with system level optimizations
    Nagarajan Kathiresan, Ramzi Temanni, Hakeem Almabrazi, Najeeb Syed, Puthen Veettil Jithesh, Rashid Al‐Ali · 2017 · Scientific Reports
65. Bioinformatics for Human Genetics: Promises and Challenges
    Annika Lindblom, Peter N. Robinson · 2011 · Human Mutation
66. Analysis of quality raw data of second generation sequencers with Quality Assessment Software
    Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro, Jan Baumbach, Vasco Azevedo, Maria PC Schneider, Artur Silva · 2011 · BMC Research Notes
67. Performance optimization in DNA short-read alignment
    Richard N. Wilton, Alexander S. Szalay · 2022 · Bioinformatics
68. Metagenomic Detection Methods in Biopreparedness Outbreak Scenarios
    Oskar Karlsson Lindsjö, Trine Hansen, Rickard Knutsson, Charlotta Löfström, Fredrik Granberg, Mikael Berg · 2013 · Biosecurity and Bioterrorism Biodefense Strategy Practice and Science
69. MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads
    Yinghua Wu, Lifeng Tian, Mario Pirastu, Dwight Stambolian, Hongzhe Li · 2013 · Frontiers in Genetics
70. Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach
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71. A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis
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72. Identification of cis-regulatory sequence variations in individual genome sequences
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73. Evaluating Performance and Portability of a core bioinformatics kernel on multiple vendor GPUs
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74. RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria
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75. Screening Metagenomic Data for Viruses Using the E-Probe Diagnostic Nucleic Acid Assay
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76. Inverse Lyndon words and inverse Lyndon factorizations of words
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77. Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities
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78. Guidelines for RNA-Seq data analysis
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79. Genome-wide identification and characterization of flavonol synthase (FLS) gene family in Brassica vegetables and their roles in response to biotic and abiotic stresses
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80. Short Read Alignment Using SOAP2
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81. Compression of next-generation sequencing quality scores using memetic algorithm
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82. An energy‐aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures
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83. A probabilistic method for the detection and genotyping of small indels from population-scale sequence data
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84. A random-permutations-based approach to fast read alignment
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85. A survey of sequence-to-graph mapping algorithms in the pangenome era
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86. MapReducing a genomic sequencing workflow
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87. Methods of privacy-preserving genomic sequencing data alignments
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88. New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies
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89. A meta-analysis and a functional study support the influence of mtDNA variant m.16519C on the risk of rapid progression of knee osteoarthritis
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90. Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
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91. Textual data compression in computational biology: Algorithmic techniques
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92. Adult Genetic Risk Screening
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93. Detection of microRNAs in color space
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94. Differential contributions of sarcomere and mitochondria-related multigene variants to the endophenotype of hypertrophic cardiomyopathy
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95. Impact of Next-Generation Whole-Exome sequencing in molecular diagnostics
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96. Parallel stochastic systems biology in the cloud
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97. A Science Gateway Cloud With Cost-Adaptive VM Management for Computational Science and Applications
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98. Querying large read collections in main memory: a versatile data structure
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99. Hadooping the genome: The impact of big data tools on biology
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100. Seq: a high-performance language for bioinformatics
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