Fast-GBS.v1
Fast-GBS is built upon standard bioinformatics language and file formats, is capable of handling data from different sequencing platforms for different species, is capable of detecting different kinds of variants (SNPs, MNPs, and Indels).
Fast-GBS.v2
The second generation of Fast-GBS (v2.0) offers several new options (e.g., processing paired-end reads and imputation of missing data) and features (e.g., summary statistics of genotypes) to improve the GBS data analysis process.
Fast-WGS
Fast-WGS is the most efficient bioinformatics pipeline to process whole-genome sequencing (WGS) data. It is capable of handling data from different sequencing platforms for different species and is capable of detecting different kinds of variants (SNPs, MNPs, and Indels).
DepthFinder
Despite the huge improvements of the reduced-representation sequencing (RRS) methods in the last decade, the estimation of the number of reads (i.e. read depth) required per sample for an efficient and effective genotyping remains mostly based on trial and error. DepthFinder, designed to estimate the required read counts for RRS methods.
SRG Extractor
SRG Extractor is a bioinformatic program designed to create a skinny reference genome (SRG) for reduced-representation sequencing (RRS) analysis.
HaplotypeMiner
HaplotypeMiner is an R package developed for exploring allelic diversity at genes of interest in a plant breeding context. The program minimally takes as input a dataset of SNP markers generated through various methods (e.g. genotyping-by-sequencing [GBS] or SNP arrays) and the genomic position of a gene of interest, and outputs a set of possible haplotypes defined by the genotypes of a reduced number of neighboring SNPs.
DelGBS
delgbs is an R package which provides tools for detecting copy number variation from genotyping-by-sequencing (GBS) data. delgbs bases its CNV calls on the number of reads per sample in discrete bins (e.g. 1-kb bins) located along a reference genome.
