ArrayMaker
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
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
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
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
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
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
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…