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Genotyping by sequencing software tools

Sequencing 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 cost-effective GBS protocol is currently being applied in numerous species by a large number of researchers. Source text: Glaubitz et al., 2014.

ArrayMaker

OMIC_08633

ArrayMaker

A user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at…

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 association analysis software and datasets…

GBStools

OMIC_10422

GBStools

A statistical method to remove errors caused by restriction site polymorphisms. We…

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 rate, and in two empirical human data sets (N = 8 and…

GBSX

OMIC_08632

GBSX

Assists in selecting the appropriate enzyme and the design of compatible in-line…

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 barcode which can easily be plugged into existing…

Haplotag

OMIC_10604

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 fulfilling the following set of criteria: (1)…

SimRAD

OMIC_09148

SimRAD

An R package that performs in silico restriction enzyme digests and fragment size…

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. In silico digestion is performed on a reference…

SNiPlay

OMIC_06478

SNiPlay

A web-based tool for detection, management and analysis of genetic variants including…

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 manage and exploit SNPs derived from next…

TASSEL-GBS

OMIC_08634

TASSEL-GBS

A bioinformatics pipeline designed for the efficient processing of raw GBS sequence data…

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) Ability to run on the modest computing resources that…