ArticlePloS one2014
TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 834 papers.
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Who cites it
834 citing papers in PubMed.
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- Review
- Pinpointing genomic regions conferring herbicide tolerance in cassava via genome-wide association mapping.Plant molecular biology · 2026Article
- Genomic evidence for widespread hybridization and demographic history in invasive saltcedar.Heredity · 2026Article
- Deciphering the genetic basis of yield components in wheat by integrating hyperspectral-based phenomes.Plant phenomics (Washington, D.C.) · 2026Article
- Development of an open-pollinated genetic mapping framework to facilitate the identification of QTL in apples.The plant genome · 2026Article
- Genome wide association studies and expression analyses identify candidate genes for spot blotch resistance in bread wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genome-wide association study in a US soft winter wheat population reveals novel and known sources of resistance to the Septoria tritici blotch pathogen Zymoseptoria tritici.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Identifying marker-trait associations for wheat stem sawfly resistance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Advances in mutant characterization for detecting causal mutations in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Genome-Wide Identification of Melon Single-Nucleotide Polymorphisms and Structural Variations Associated with Resistance toPlants (Basel, Switzerland) · 2026Article
- Improving genomic prediction in wheat with random regression models with genotype-specific phenology-driven environmental covariates.The plant genome · 2026Article
- Identification of candidate loci for leafing date in Iranian walnut germplasm collection using GBS-GWAS approach and validation by SNaPshot.BMC plant biology · 2026Article
- First brassinosteroid-based dwarf mutant discovered and characterized in grapevine.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Unveiling the genetic diversity and ancestry ofAoB PLANTS · 2026Article
- Dissecting the genetic basis of relevant fruit quality traits in interspecific grapevines (Horticulture research · 2026Article
- A haplotype-resolved genome assembly of hexaploid Kentucky-31 tall fescue (Lolium arundinaceum).G3 (Bethesda, Md.) · 2026Article
- Genome-wide association study identifies consistent genomic loci for yield and nutritional quality in Ethiopian sorghum landraces.The plant genome · 2026Article
774 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. Herein we describe a bioinformatics pipeline, TASSEL-GBS, 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 are typically available to small breeding or ecological research programs, including desktop or laptop machines with only 8-16 GB of RAM, (2) Scalability from small to extremely large studies, where hundreds of thousands or even millions of SNPs can be scored in up to 100,000 individuals (e.g., for large breeding programs or genetic surveys), and (3) Applicability in an accelerated breeding context, requiring rapid turnover from tissue collection to genotypes. Although a reference genome is required, the pipeline can also be run with an unfinished "pseudo-reference" consisting of numerous contigs. We describe the TASSEL-GBS pipeline in detail and benchmark it based upon a large scale, species wide analysis in maize (Zea mays), where the average error rate was reduced to 0.0042 through application of population genetic-based SNP filters. Overall, the GBS assay and the TASSEL-GBS pipeline provide robust tools for studying genomic diversity.
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