msgbsR: an R package to analyse methylation sensitive genotyping by sequencing (MS-GBS) data
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چکیده
منابع مشابه
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and ...
متن کاملPotential of low-coverage genotyping-by-sequencing and imputation for cost-effective genomic selection in bi-parental segregating populations
Genotyping-by-sequencing (GBS) is an alternative genotyping method to singlenucleotide polymorphism (SNP) arrays that has received considerable attention in the plant breeding community. In this study we use simulation to quantify the potential of lowcoverage GBS and imputation for cost-effective genomic selection in biparental segregating populations. The simulations comprised a range of scena...
متن کاملGenotyping-by-Sequencing for Populus Population Genomics: An Assessment of Genome Sampling Patterns and Filtering Approaches
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and ...
متن کاملGenotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping
Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome...
متن کاملPhased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize
High-throughput sequencing (HTS) of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken from heterogeneous populations of heterozygous individuals. This requires that a number of iss...
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