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Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.ympev.2011.12.007openalex-snapshot
Applications of next-generation sequencing to phylogeography and phylogenetics
inferredcites →https://doi.org/10.1038/nature08670openalex-snapshot
Genome sequence of the palaeopolyploid soybean
inferredcites →https://doi.org/10.1038/nature10242openalex-snapshot
An integrated semiconductor device enabling non-optical genome sequencing
inferredcites →https://doi.org/10.1038/nrg2986openalex-snapshot
Genotype and SNP calling from next-generation sequencing data
inferredcites →https://doi.org/10.1038/nrg3012openalex-snapshot
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btm308openalex-snapshot
TASSEL: software for association mapping of complex traits in diverse samples
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1101/gr.115402.110openalex-snapshot
Multiplexed shotgun genotyping for rapid and efficient genetic mapping
inferredcites →https://doi.org/10.1101/gr.5681207openalex-snapshot
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
inferredcites →https://doi.org/10.1111/eva.12128openalex-snapshot
Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05513.xopenalex-snapshot
Genome‐wide association genetics of an adaptive trait in lodgepole pine
inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot
Stacks: an analysis tool set for population genomics
inferredcites →https://doi.org/10.1155/2012/831460openalex-snapshot
SNP Discovery through Next-Generation Sequencing and Its Applications
inferredcites →https://doi.org/10.1186/s12859-015-0514-3openalex-snapshot
GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments
inferredcites →https://doi.org/10.1201/9781315365084-7openalex-snapshot
SNP Discovery Through Next-Generation Sequencing and Its Applications
inferredcites →https://doi.org/10.1371/journal.pgen.1003215openalex-snapshot
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
inferredcites →https://doi.org/10.1371/journal.pone.0001172openalex-snapshot
Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1371/journal.pone.0032253openalex-snapshot
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach
inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
inferredcites →https://doi.org/10.1371/journal.pone.0037565openalex-snapshot
Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations
inferredcites →https://doi.org/10.1371/journal.pone.0054603openalex-snapshot
An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping
inferredcites →https://doi.org/10.1371/journal.pone.0076925openalex-snapshot
Application of Genotyping-by-Sequencing on Semiconductor Sequencing Platforms: A Comparison of Genetic and Reference-Based Marker Ordering in Barley
inferredcites →https://doi.org/10.1371/journal.pone.0090346openalex-snapshot
TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline
inferredcites →https://doi.org/10.1371/journal.pone.0131533openalex-snapshot
Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0132112openalex-snapshot
Exploring and Mobilizing the Gene Bank Biodiversity for Wheat Improvement
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Hydrolysis probe-based real-time PCR as an SNP genotyping method: an application in pharmacogenetic study of lung cancer patients
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Recent Advances and Applicability of GBS, GWAS, and GS in Soybean
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Opportunity and Challenges for High‐throughput Genotyping in Sugarcane
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Effects of Different SNP Calling and Sequence Mapping Choices on the Inference of Genetic Architecture Underlying Migration Tendency
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Genotyping-by-Sequencing on the Ion Torrent Platform in Barley
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A novel diagnostic SNP panel for fishery management of green abalone (Haliotis fulgens).
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Spatial genetic structure at the leading edge of a spruce budworm outbreak: The role of dispersal in outbreak spread
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DArTseq-generated SNPs revealed low genetic diversity and genetic erosion along life stages in fragmented populations of Afrocarpus gracilior (Pilg.) C.N.Page in southern Ethiopia
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The use of pinned specimens helps uncover patterns of genetic differentiation and signatures of selection in a wild pollinator
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The development of liquid-phase chip by target sequencing and their application in watermelon molecular breeding
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SNP discovery and applications in plant genetics for sustainable food security: A review
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Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes
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The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform
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Diversity and structure assessment of the genetic resources in a germplasm collection from a vanilla breeding programme in Madagascar
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Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
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Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset
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GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars
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Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.)
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High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome
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Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)
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Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance
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Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation
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Genome-wide diversity analysis to infer population structure and linkage disequilibrium among Colombian coconut germplasm
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Evaluating the performance of low-frequency variant calling tools for the detection of variants from short-read deep sequencing data
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Genotyping by sequencing reveals a chromosome A04 QTL governing whitefly resistance in upland cotton
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Skim-Nanopore sequencing for routine genomic evaluation and bacterial pathogen detection in cattle
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Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing
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SRG extractor: a skinny reference genome approach for reduced-representation sequencing
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Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia
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Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (Triticum aestivum)
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Development of a genome‐wide 200K SNP array and its application for high‐density genetic mapping and origin analysis of Camellia sinensis
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Systematic exploration of Ziziphus species collection and gene identification influencing physiological traits using genotype‐by‐sequencing technology
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Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species
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Linkage mapping and quantitative trait loci analysis of sweetness and other fruit quality traits in papaya
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Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
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Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao
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Dartseq-Generated Snps Revealed Low Genetic Diversity and Genetic Erosion Along Life Stages in Fragmented Populations of Afrocarpus Gracilior (Pilg.) C.N.Page in Southern Ethiopia
inferred← citeshttps://doi.org/10.22267/rcia.183502.92openalex-snapshot
Uso de las ciencias ómicas para el mejoramiento genético de cultivos
inferred← citeshttps://doi.org/10.2478/aoas-2022-0063openalex-snapshot
Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection
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Phylogenetic relationships, population connectivity, and development of genetic assignment testing in Buller's Albatross (Thalassarche bulleri ssp.)
inferred← citeshttps://doi.org/10.26686/wgtn.17136056openalex-snapshot
Patterns of population genetic structure and connectivity of squat lobsters associated with vulnerable marine ecosystems
inferred← citeshttps://doi.org/10.26686/wgtn.24041817openalex-snapshot
Population genetic and genomic approaches for the management of the blackfoot paua, Haliotis iris Gmelin 1791, within the genus context
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Speciation and hybridization in Jamaican-endemic Streamertail Hummingbirds (Trochilus polytmus and T. scitulus)
inferred← citeshttps://doi.org/10.33545/26174693.2024.v8.i8f.1771openalex-snapshot
Next-gen breeding: The impact of phenotyping and genotyping on crop improvement
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Genetic Diversity Analysis of Olive Germplasm (Olea europaea L.) With Genotyping-by-Sequencing Technology
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Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing
inferred← citeshttps://doi.org/10.3389/fpls.2017.02227openalex-snapshot
Genetic Architecture of Capitate Glandular Trichome Density in Florets of Domesticated Sunflower (Helianthus annuus L.)
inferred← citeshttps://doi.org/10.3389/fpls.2018.01809openalex-snapshot
Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola
inferred← citeshttps://doi.org/10.3389/fpls.2021.618245openalex-snapshot
Analysis of Genetic Diversity and Population Structure of Orobanche foetida Populations From Tunisia Using RADseq
inferred← citeshttps://doi.org/10.3389/fpls.2021.626811openalex-snapshot
Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations
inferred← citeshttps://doi.org/10.3389/fpls.2021.628439openalex-snapshot
The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions
inferred← citeshttps://doi.org/10.3389/fpls.2022.811312openalex-snapshot
Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China
inferred← citeshttps://doi.org/10.3389/fpls.2022.931423openalex-snapshot
Genotyping by Sequencing Advancements in Barley
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Development of the maize 5.5K loci panel for genomic prediction through genotyping by target sequencing
inferred← citeshttps://doi.org/10.3390/agronomy9090484openalex-snapshot
Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden
inferred← citeshttps://doi.org/10.3390/ani11082226openalex-snapshot
In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data
inferred← citeshttps://doi.org/10.3390/books978-3-03842-004-0openalex-snapshot
Plant Genetics and Biotechnology in Biodiversity
inferred← citeshttps://doi.org/10.3390/d9030038openalex-snapshot
NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops
inferred← citeshttps://doi.org/10.3390/f12020222openalex-snapshot
Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods
inferred← citeshttps://doi.org/10.3390/genes10110846openalex-snapshot
The Value of Reference Genomes in the Conservation of Threatened Species
inferred← citeshttps://doi.org/10.3390/ijms22084219openalex-snapshot
TILLING-by-Sequencing+ to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis
inferred← citeshttps://doi.org/10.3390/life16030521openalex-snapshot
Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement
inferred← citeshttps://doi.org/10.3390/molecules31111786openalex-snapshot
Integrating GBS-Derived SNP Markers with Phytochemical Profiling and Anti-Obesity Enzyme Inhibition in Phyllanthus emblica
inferred← citeshttps://doi.org/10.3390/plants11162172openalex-snapshot
Construction of A GBS-Based High-Density Genetic Map and Flower Color-Related Loci Mapping in Grasspea (Lathyrus sativus L.)
inferred← citeshttps://doi.org/10.3390/plants11182385openalex-snapshot
Evidence of Asexual Overwintering of Melampsora paradoxa and Mapping of Stem Rust Host Resistance in Salix
inferred← citeshttps://doi.org/10.3390/plants13141910openalex-snapshot
Somatic Mutation Accumulations in Micropropagated Cannabis Are Proportional to the Number of Subcultures
inferred← citeshttps://doi.org/10.3390/plants14132051openalex-snapshot
Dwarf Mistletoes (Arceuthobium, Viscaceae) of North America: Classification Systems, Phylogenetic Relationships, and Taxonomic Characteristics
inferred← citeshttps://doi.org/10.4018/979-8-3693-8603-3.ch005openalex-snapshot
Genome-Wide Association Study (GWAS) for Economically Important Traits in Canola (Brassica napus L.)
inferred← citeshttps://doi.org/10.6084/m9.figshare.13279433openalex-snapshot
Additional file 1 of Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
inferred← citeshttps://doi.org/10.6084/m9.figshare.13279436openalex-snapshot
Additional file 2 of Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
inferred← citeshttps://doi.org/10.6084/m9.figshare.13279439openalex-snapshot
Additional file 3 of Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
inferred← citeshttps://doi.org/10.6084/m9.figshare.13279442openalex-snapshot
Additional file 4 of Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm
inferred← citeshttps://doi.org/10.6084/m9.figshare.14151058openalex-snapshot
Additional file 1 of Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species
inferred← citeshttps://doi.org/10.6084/m9.figshare.14151061openalex-snapshot
Additional file 2 of Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species
inferred← citeshttps://doi.org/10.6084/m9.figshare.14151064openalex-snapshot
Additional file 3 of Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species
inferred← citeshttps://doi.org/10.64898/2026.09.26.754587openalex-snapshot
QuImputer: an LD-informed QUBO/Ising formulation of genotype imputation with quantum-hardware execution
inferred← citeshttps://doi.org/10.70675/3b37585bzc9b3z4bc5za4c1zd35513003ea3openalex-snapshot
Génomique de l'adaptation de Globodera pallida aux résistances de la pomme de terre et conséquences sur les traits d'histoire de vie du nématode
inferred← citeshttps://doi.org/10.9787/kjbs.2021.53.2.116openalex-snapshot
Development of Single Nucleotide Polymorphism Markers Linked to Quantitative Trait Loci Controlling Anthocyanin Content in Red Bulb Onion ( Allium cepa L.)
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