title: Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data.
abstract: BACKGROUND
  Next-generation sequencing (NGS) technologies have accelerated considerably the investigation into the composition of genomes and their functions. Genotyping-by-sequencing (GBS) is a genotyping approach that makes use of NGS to rapidly and economically scan a genome. It has been shown to allow the simultaneous discovery and genotyping of thousands to millions of SNPs across a wide range of species. For most users, the main challenge in GBS is the bioinformatics analysis of the large amount of sequence information derived from sequencing GBS libraries in view of calling alleles at SNP loci. Herein we describe a new GBS bioinformatics pipeline, Fast-GBS, designed to provide highly accurate genotyping, to require modest computing resources and to offer ease of use.
  
  
  RESULTS
  Fast-GBS is built upon standard bioinformatics language and file formats, is capable of handling data from different sequencing platforms, is capable of detecting different kinds of variants (SNPs, MNPs, and Indels). To illustrate its performance, we called variants in three collections of samples (soybean, barley, and potato) that cover a range of different genome sizes, levels of genome complexity, and ploidy. Within these small sets of samples, we called 35 k, 32 k and 38 k SNPs for soybean, barley and potato, respectively. To assess genotype accuracy, we compared these GBS-derived SNP genotypes with independent data sets obtained from whole-genome sequencing or SNP arrays. This analysis yielded estimated accuracies of 98.7, 95.2, and 94% for soybean, barley, and potato, respectively.
  
  
  CONCLUSIONS
  We conclude that Fast-GBS provides a highly efficient and reliable tool for calling SNPs from GBS data.
authors.affiliation: Département de Phytologie, Université Laval, Quebec City, QC, Canada.|Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.
authors.forename: Davoud
authors.initials: D
authors.lastname: Torkamaneh
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Laroche
authors.affiliation: Département de Phytologie, Université Laval, Quebec City, QC, Canada.|Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.
authors.forename: Maxime
authors.initials: M
authors.lastname: Bastien
authors.affiliation: Département de Phytologie, Université Laval, Quebec City, QC, Canada.|Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada.
authors.forename: Amina
authors.initials: A
authors.lastname: Abed
authors.affiliation: Département de Phytologie, Université Laval, Quebec City, QC, Canada. francois.belzile@fsaa.ulaval.ca.|Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada. francois.belzile@fsaa.ulaval.ca.
authors.forename: François
authors.initials: F
authors.lastname: Belzile
mesh_terms: D000483:Alleles; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D018745:Genome, Plant; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D001467:Hordeum / Q000235:genetics; D020407:Internet; D020641:Polymorphism, Single Nucleotide; D013025:Glycine max / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D004247:DNA
keywords: Bioinformatics pipeline; GBS; Genotype accuracy; NGS; SNP