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"polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids". Preprint on bioRxiv.
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Clark, Lindsay V.; Dwiyanti, Maria S.; Anzoua, Kossonou G.; Brummer, Joe E.; Głowacka, Katarzyna; Hall, Megan; Heo, Kweon; Jin, Xiaoli; Lipka, Alexander E.; Peng, Junhua; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P.; Sacks, Erik J. (2017): "Data from: Genome-wide association and genomic prediction for biomass yield in Miscanthus sinensis phenotyped in Asia and North America". University of Illinois at Urbana-Champaign.
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Clark, L.V. "polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids". R package archived at Zenodo.
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Money, D. "LinkImpute: fast and accurate genotype imputation for non-model organisms."
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Clark, Lindsay V.; Dwiyanti, Maria Stefanie; Anzoua, Kossonou G.; Brummer, Joe E.; Glowacka, Katarzyna; Hall, Megan; Heo, Kweon; Jin, Xiaoli; Lipka, Alexander E.; Peng, Junhua; Yamada, Toshihiko; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P.; Sacks, Erik J. (2019): "RAD-seq genotypes for a Miscanthus sinensis diversity panel". University of Illinois at Urbana-Champaign.
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Dataset Description
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This set of scripts accompanies the manuscript describing the R package polyRAD, which uses DNA sequence read depth to estimate allele dosage in diploids and polyploids. Using several high-confidence SNP datasets from various species, allelic read depth from a typical RAD-seq dataset was simulated, then genotypes were estimated with polyRAD and other software and compared to the true genotypes, yielding error estimates.
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Subject
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Life Sciences
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Keywords
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R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
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License
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CC BY
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Funder
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U.S. National Science Foundation (NSF)
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Grant:
1661490
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Corresponding Creator
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Lindsay V. Clark
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