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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…
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GBS-SNP-CROP
Desktop

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…

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SNiPlay
Web

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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GBSX
Desktop

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…

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SimRAD
Desktop

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.…

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GBStools
Desktop

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…

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TASSEL-GBS
Desktop

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)…

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ArrayMaker
Desktop

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…

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msgbsR
Desktop

msgbsR

Permits to proceed analysis of a methylation sensitive genotyping by sequencing…

Permits to proceed analysis of a methylation sensitive genotyping by sequencing (MS-GBS) experiment. msgbsR is able to read counts and cut sites from a MS-GBS experiment.

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Haplotag
Desktop

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…

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