Genotyping by sequencing (GBS) is a next generation sequencing based method that takes advantage of reduced representation to enable high throughput genotyping of large numbers of individuals at a large number of SNP markers. The relatively straightforward, robust, and cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers.
Source text:
(Glaubitz et al., 2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One.
Discovers SNP and characterizes plant germplasm. GBS-SNP-CROP adopts a…
Discovers SNP and characterizes plant germplasm. GBS-SNP-CROP adopts a clustering strategy to build a population-tailored “Mock Reference” from the same GBS data used for downstream SNP calling…
A web-based tool for detection, management and analysis of genetic variants…
A web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily…
Assists in selecting the appropriate enzyme and the design of compatible…
Assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, GBSX performs optimized demultiplexing using these barcodes to create fastq files per…
An R package that performs in silico restriction enzyme digests and fragment…
An R package that performs in silico restriction enzyme digests and fragment size selection as implemented in most restriction site associated DNA polymorphism and genotyping by sequencing methods.…
A statistical method to remove errors caused by restriction site polymorphisms.…
A statistical method to remove errors caused by restriction site polymorphisms. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation…
A bioinformatics pipeline designed for the efficient processing of raw GBS…
A bioinformatics pipeline designed for the efficient processing of raw GBS sequence data into SNP genotypes. The TASSEL-GBS pipeline successfully fulfills the following key design criteria: (1)…
A user-friendly tool that extracts accurate single nucleotide polymorphism…
A user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with…
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