Genotype and SNP calling from next-generation sequencing data

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Items 201–300 of 1,000

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2. Review of alignment and SNP calling algorithms for next-generation sequencing data
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3. Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity
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4. Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity
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5. Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon
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6. Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage
   Chodon Sass, William J. D. Iles, Craig F. Barrett, Selena Y. Smith, Chelsea Dvorak Specht · 2016 · PeerJ
7. A comparative assessment of SNP and microsatellite markers for assigning parentage in a socially monogamous bird
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8. Integrating imaging and omics data: A review
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9. Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs
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10. RADseq approaches and applications for forest tree genetics
    Thomas Lee Parchman, Joshua P. Jahner, Kathryn A. Uckele, Lanie M. Galland, Andrew J. Eckert · 2018 · Tree Genetics & Genomes
11. The molecular genetic basis of herbivory between butterflies and their host plants
    Sumitha Nallu, Jason A. Hill, Kristine Don, Carlos Sahagun, Wei Zhang, Camille Meslin, Emilie C. Snell‐Rood, Nathan L Clark, Nathan I. Morehouse, Joy M. Bergelson et al. · 2018 · Nature Ecology & Evolution
12. Dissecting spatiotemporal biomass accumulation in barley under different water regimes using high‐throughput image analysis
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13. Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
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14. Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination
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15. snpAD: an ancient DNA genotype caller
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16. Towards a molecular characterization of autism spectrum disorders: an exome sequencing and systems approach
    Joon‐Yong An, Alexandre S. Cristino, Qiongyi Zhao, Janette Edson, S. M. Williams, David Ravine, John A. Wray, Vikki M. Marshall, A Hunt, Andrew Whitehouse et al. · 2014 · Translational Psychiatry
17. Next–generation sequencing and systematics: What can a billion base pairs of DNA sequence data do for you?
    Nicola Harrison, Catherine Anne Kidner · 2011 · Taxon
18. Intra‐individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?
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19. Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics
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20. The coexistence of copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) at a locus can result in distorted calculations of the significance in associating SNPs to disease
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21. Forensic genealogy—A comparison of methods to infer distant relationships based on dense SNP data
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22. Microevolution of Serial Clinical Isolates ofCryptococcus neoformansvar.grubiiandC. gattii
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23. Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage
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24. SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming
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25. Critical review of NGS analyses for de novo genotyping multigene families
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26. Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis
    Tania Wyss, Frédéric G. Masclaux, Pawel Rosikiewicz, Marco Pagni, Ian R. Sanders · 2016 · The ISME Journal
27. The Role of Next-Generation Sequencing in Pharmacogenetics and Pharmacogenomics
    Ute I. Schwarz, Markus Gulilat, Richard B. Kim · 2018 · Cold Spring Harbor Perspectives in Medicine
28. RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis
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29. Halvade: scalable sequence analysis with MapReduce
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30. Northern glacial refugia and altitudinal niche divergence shape genome‐wide differentiation in the emerging plant model Arabidopsis arenosa
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31. SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data
    Paul D. Blischak, Laura Salter Kubatko, Andrea D. Wolfe · 2017 · Bioinformatics
32. De novo transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set
    Sonal Singhal · 2013 · Molecular Ecology Resources
33. Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories
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34. Comparison of three variant callers for human whole genome sequencing
    Anna Maria Supernat, Oskar Valdimar Vidarsson, Vidar Martin Steen, Tomasz Stokowy · 2018 · Scientific Reports
35. Single-nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska
    Wesley A. Larson, James E. Seeb, Carita E. Pascal, William David Templin, Lisa Wishard Seeb · 2014 · Canadian Journal of Fisheries and Aquatic Sciences
36. ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis
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37. Whole genome sequencing in the prevention and control of Staphylococcus aureus infection
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38. Development and implementation of genomic predictions in beef cattle
    Donagh Pearse Berry, José Fernando Garcia, Dorian J. Garrick · 2016 · Animal Frontiers
39. Multiple Origin but Single Domestication Led to Oryza sativa
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40. Molecular quantitative genetics
    Henrik Jensen, Marta Szulkin, Jon Slate · 2014 · Oxford University Press eBooks
41. Techniques in bacterial strain typing: past, present, and future
    Shelby R. Simar, Blake Hanson, César A. Arias · 2021 · Current Opinion in Infectious Diseases
42. Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics
    Ying Chun Lu, Mengfei Li, Zhendong Gao, Hongming Ma, Yuqing Chong, Jieyun Hong, Jiao Wu, Dongwang Wu, Dongmei Xi, Weidong Deng · 2025 · International Journal of Molecular Sciences
43. Construction of a SNP and SSR linkage map in autotetraploid blueberry using genotyping by sequencing
    Susan McCallum, Julie Graham, Linzi Jorgensen, Lisa J. Rowland, Nahla Victor Bassil, James F. Hancock, Edmund J. Wheeler, Kelly J. Vining, Jesse Poland, James W. Olmstead et al. · 2016 · Molecular Breeding
44. Fastq_clean: An optimized pipeline to clean the Illumina sequencing data with quality control
    Mi Zhang, Honghe Sun, Zhangjun Fei, Feng Zhan, Xiujun Gong, Shan Gao · 2014 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
45. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking
    Rafaela Gomes Ferrari, Pedro Panzenhagen, Carlos Adam Conte‐Júnior · 2017 · Frontiers in Microbiology
46. High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
    Fábio Pértille, Carlos Guerrero‐Bosagna, Vinicius Henrique da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, Luiz Lehmann Coutinho · 2016 · Scientific Reports
47. Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data
    James A. Cahill, André E. R. Soares, Richard Edward Green, Beth Shapiro · 2016 · Philosophical Transactions of the Royal Society B Biological Sciences
48. Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
    Marie A. Brunet, Sébastien A. Levesque, Darel John Hunting, Alan Arthur Cohen, Xavier Roucou · 2018 · Genome Research
49. Signatures of balancing selection in toll-like receptor (TLRs) genes – novel insights from a free-living rodent
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50. Genome-wide signatures of the geographic expansion and breeding of soybean
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51. Impact of three Illumina library construction methods on GC bias and HLA genotype calling
    James H. Lan, Yuxin Yin, Elaine F. Reed, Kevin Moua, Kimberly A. Thomas, Qiuheng Zhang · 2014 · Human Immunology
52. Human Germline Mutation and the Erratic Evolutionary Clock
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53. The complex geography of domestication of the African rice Oryza glaberrima
    Choi, Jae Young, Zaidem, Maricris, Gutaker, Rafal, Dorph, Katherine, Singh, Rakesh Kumar, Purugganan, Michael D. · 2019 · PLoS Genetics
54. Comparing somatic mutation-callers: beyond Venn diagrams
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55. Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia)
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56. Human genome variability, natural selection and infectious diseases
    Matteo Fumagalli, Manuela Sironi · 2014 · Current Opinion in Immunology
57. Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates
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58. Characterization and comparison of human nuclear and cytosolic editomes
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59. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment
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60. Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass ( L olium perenne ( L .))
    Matthew Hegarty, R. S. Yadav, Michael R. F. Lee, Ian Armstead, Ruth Sanderson, Nigel David Scollan, Wayne Powell, Leif Skøt · 2013 · Plant Biotechnology Journal
61. Palindromic Molecule Beacon-Based Cascade Amplification for Colorimetric Detection of Cancer Genes
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62. Systematic benchmark of ancient DNA read mapping
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63. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes
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64. Evidence for Increased Levels of Positive and Negative Selection on the X Chromosome versus Autosomes in Humans
    Krishna R. Veeramah, Ryan N. Gutenkunst, August E. Woerner, Joseph C. Watkins, Michael F. Hammer · 2014 · Molecular Biology and Evolution
65. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals
    Kristina M. Cammen, Kimberly R. Andrews, Emma L. Carroll, Andrew David Foote, Emily Humble, Jane I. Khudyakov, Marié Louis, Michael R. McGowen, Morten Tange Olsen, Amy M. Van Cise · 2016 · Journal of Heredity
66. Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
    Wengang Zhang, Junya Li, Yong Guo, Lupei Zhang, Lingyang Xu, Xue Gao, Bo Zhu, Huijiang Gao, Hemin Ni, Yan Chen · 2016 · Scientific Reports
67. Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes
    Hannes Svardal, Walter Salzburger, Milan Malinsky · 2020 · Annual Review of Animal Biosciences
68. Out of Southern East Asia of the Brown Rat Revealed by Large-Scale Genome Sequencing
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69. Accounting for uncertainty in DNA sequencing data
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70. The struggle to find reliable results in exome sequencing data: filtering out Mendelian errors
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71. Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data
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72. BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower
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73. A Whole-Chromosome Analysis of Meiotic Recombination inDrosophila melanogaster
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74. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards
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75. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™
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76. Estimating genotyping errors from genotype and reconstructed pedigree data
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77. Microbial sequence typing in the genomic era
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78. From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
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79. Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera
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80. QTL underlying some agronomic traits in barley detected by SNP markers
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81. Comprehensive description of genomewide nucleotide and structural variation in short‐season soya bean
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82. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge
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83. Computational and Bioinformatics Frameworks for Next‐Generation Whole Exome and Genome Sequencing
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84. VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering
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85. SorGSD: a sorghum genome SNP database
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86. Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data
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87. Trade‐offs and utility of alternative RADseq methods: Reply to Puritz et al .
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88. Lessons from next-generation sequencing analysis in hematological malignancies
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89. Whole-Genome Sequencing of Tibetan Macaque (Macaca thibetana) Provides New Insight into the Macaque Evolutionary History
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90. AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications
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91. Genotyping‐by‐sequencing for estimating relatedness in nonmodel organisms: Avoiding the trap of precise bias
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92. Local adaptation and ecological differentiation under selection, migration, and drift inArabidopsis lyrata*
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93. Computational analysis of next generation sequencing data and its applications in clinical oncology
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94. Next-Generation Sequencing for Clinical Management of Multiple Myeloma: Ready for Prime Time?
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95. Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach
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96. Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation
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97. Estimating and accounting for genotyping errors in RAD‐seq experiments
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98. Postzygotic single-nucleotide mosaicisms in whole-genome sequences of clinically unremarkable individuals
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99. Lossy compression of quality scores in genomic data
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100. WEP: a high-performance analysis pipeline for whole-exome data
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