Genotype and SNP calling from next-generation sequencing data

Cited by (1,000)

Items 101–200 of 1,000

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5. The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments
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9. Interspecific Gene Flow Shaped the Evolution of the Genus Canis
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10. Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons
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11. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies
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12. Classification and Characterization of Species within the Genus Lens Using Genotyping-by-Sequencing (GBS)
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14. Next-generation sequencing technologies and applications for human genetic history and forensics
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15. Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids
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18. Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map
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19. Effective filtering strategies to improve data quality from population-based whole exome sequencing studies
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24. What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species
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26. Potential of genotyping-by-sequencing for genomic selection in livestock populations
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27. Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
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28. A beginners guide to SNP calling from high-throughput DNA-sequencing data
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29. A genome-wide study of Hardy–Weinberg equilibrium with next generation sequence data
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30. Comprehensive analysis of RNA-protein interactions by high-throughput sequencing–RNA affinity profiling
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31. Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data
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32. An ultra-high-density bin map facilitates high-throughput QTL mapping of horticultural traits in pepper ( Capsicum annuum )
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33. From next-generation resequencing reads to a high-quality variant data set
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34. polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
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35. Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™
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36. Accuracy and efficiency of germline variant calling pipelines for human genome data
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37. Multilocus Detection of Wolf x Dog Hybridization in Italy, and Guidelines for Marker Selection
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38. GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data
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39. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data
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40. Methods for diversity and overlap analysis in T-cell receptor populations
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41. Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut
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42. The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment
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43. Best Practice Guidelines for the Use of Next-Generation Sequencing Applications in Genome Diagnostics: A National Collaborative Study of Dutch Genome Diagnostic Laboratories
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44. SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?
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45. STRait Razor: A length-based forensic STR allele-calling tool for use with second generation sequencing data
    David H. Warshauer, David Lin, Kumar L Hari, Ravi Jain, Carey P. Davis, Bobby LaRue, Jonathan L. King, Bruce Budowle · 2013 · Forensic Science International Genetics
46. snpTree - a web-server to identify and construct SNP trees from whole genome sequence data
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47. ATLAS: Analysis Tools for Low-depth and Ancient Samples
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48. SNP genotyping and population genomics from expressed sequences – current advances and future possibilities
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49. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the N orth A merican tiger salamander ( A mbystoma tigrinum) species complex
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50. Regulatory variants: from detection to predicting impact
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51. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
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52. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities
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53. Exome sequencing explained: a practical guide to its clinical application
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54. Runs of homozygosity have utility in mammalian conservation and evolutionary studies
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55. Interpretable genotype-to-phenotype classifiers with performance guarantees
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56. Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies
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57. Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
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59. Development of the catfish 250K SNP array for genome-wide association studies
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60. Disentangling structural genomic and behavioural barriers in a sea of connectivity
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63. DNA Sequencing
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64. Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
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65. Data integration and predictive modeling methods for multi-omics datasets
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66. Arctic-adapted dogs emerged at the Pleistocene–Holocene transition
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67. A new approach for detecting low-level mutations in next-generation sequence data
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68. Droplet barcoding for massively parallel single-molecule deep sequencing
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69. Population genomics of grey wolves and wolf-like canids in North America
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70. HLA typing by next‐generation sequencing – getting closer to reality
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71. Statistical Methods in Integrative Genomics
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73. Targeted next generation sequencing as a tool for precision medicine
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75. Sequencing consolidates molecular markers with plant breeding practice
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79. Characterizing bias in population genetic inferences from low-coverage sequencing data
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80. Evaluation of model fit of inferred admixture proportions
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81. Sampling strategies for frequency spectrum-based population genomic inference
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83. Detection, Characterization, and Typing of Shiga Toxin-Producing Escherichia coli
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84. The Role and Challenges of Exome Sequencing in Studies of Human Diseases
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85. Large-Scale Mass Spectrometric Detection of Variant Peptides Resulting from Nonsynonymous Nucleotide Differences
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88. Population genomic analyses from low‐coverage RAD ‐Seq data: a case study on the non‐model cucurbit bottle gourd
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93. Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses
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98. Molecular evolutionary and population genomic analysis of the nine‐spined stickleback using a modified restriction‐site‐associated DNA tag approach
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