ArticleBMC bioinformatics2017
Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Micropropagation of Cannabis sativa: genetic and epigenetic stability assessment over multiple generations.Journal of cannabis research · 2026Article
- Population structure and genetic diversity of Phakopsora pachyrhizi in the Southeastern United States.G3 (Bethesda, Md.) · 2026Article
- Genetic mapping of quantitative trait loci associated with nematode resistance in melon using genotyping-by-sequencing.Frontiers in plant science · 2026Article
- QTL-seq analysis of seed protein quantity and quality traits in two soybean recombinant inbred line populations.Frontiers in plant science · 2026Article
- Genotyping by sequencing reveals a chromosome A04 QTL governing whitefly resistance in upland cotton.Scientific reports · 2025Article
- SimGBS: a rapid method for simulating large-scale genotyping-by-sequencing data.BMC bioinformatics · 2025Article
- Genome-Wide, High-Density Genotyping Approaches for Plant Germplasm Characterisation (Methods and Applications).International journal of molecular sciences · 2025Review
- Genome-wide association analysis of winter survival in a diverse Canadian winter wheat population.The plant genome · 2025Article
- Assigning Phenologically Asynchronous Moths to Source Populations Using Individual Genotypes.Molecular ecology · 2025Article
- Genetic diversity and population structure analysis in Asparagus officinalis.Journal, genetic engineering & biotechnology · 2025Article
- Tracking the North American Asian Longhorned Beetle Invasion With Genomics.Evolutionary applications · 2024Article
- Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused byPlants (Basel, Switzerland) · 2024Article
- Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association.BMC plant biology · 2024Article
- Genetics of flight in spongy moths (Lymantria dispar ssp.): functionally integrated profiling of a complex invasive trait.BMC genomics · 2024Article
- Integrated eQTL mapping approach reveals genomic regions regulating candidate genes of theFrontiers in plant science · 2024Article
- Dissection of theFrontiers in plant science · 2024Article
- Application of SVR-Mediated GWAS for Identification of Durable Genetic Regions Associated with Soybean Seed Quality Traits.Plants (Basel, Switzerland) · 2023Article
- Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii.Journal of advanced research · 2023Article
- An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.G3 (Bethesda, Md.) · 2023Article
- The Genotypic Variability among Short-Season Soybean Cultivars for Nitrogen Fixation under Drought Stress.Plants (Basel, Switzerland) · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-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.
resultsFast-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.
conclusionsWe conclude that Fast-GBS provides a highly efficient and reliable tool for calling SNPs from GBS data.
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