Genotyping by sequencing data analysis bioinformatics software tools
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…
Desktop app
G T A T C G C T A GBS SNP Calling… GBS SNP Calling Reference Optional Pipeline

GBS-SNP-CROP GBS SNP Calling Reference Optional Pipeline

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…

Desktop app
G T A T C G C T A Haplotag Haplotag

Haplotag

A software application designed to analyze and report results of…

A software application designed to analyze and report results of genotyping-by-sequencing. Haplotag operates with minimal user-investment on widely-available computer platforms. Haplotag is unique in…

Desktop app
G T A T C G C T A GBStools GBStools

GBStools

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…

Desktop app
G T A T C G C T A SimRAD SimRAD

SimRAD

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.…

Desktop app
G T A T C G C T A TASSEL-GBS TASSEL-GBS

TASSEL-GBS

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)…

Desktop app
G T A T C G C T A ArrayMaker ArrayMaker

ArrayMaker

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…

Desktop app
G T A T C G C T A GBSX GBSX

GBSX

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…

Web app
G T A T C G C T A SNiPlay SNiPlay

SNiPlay

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…

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