|
|
|
Related
Dataset
|
Song, Q., Hyten, D. L., Jia, G., Quigley, C. V., Fickus, E. W., Nelson, R. L., and Cregan, P. B. (2015) Genotypes of the USDA Soybean Germplasm Collection using the SoySNP50K iSelect BeadChip.
|
|
Related
Dataset
|
U. S. National Plant Germplasm System, Advanced Query of GRIN-Global Species Data.
|
|
Related
Dataset
|
Genome Database for Rosaceae
|
|
Related
Dataset
|
Solanaceae Coordinated Agricultural Project. Potato Infinium SNP Platform: Potato diversity panel dosage genotype scores.
|
|
Related
Article
|
"polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids". Preprint on bioRxiv.
|
|
Related
Dataset
|
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.
|
|
Related
Dataset
|
Liu, S., Clark, L. V., Swaminathan, K., Gifford, J. M., Juvik, J. A., and Sacks, E.J. (2016) "Data from: High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe".
|
|
Related
Article
|
da Silva, W. L., Ingram, J., Hackett, C. A., Coombs, J. J., Douches, D., Bryan, G. J., De Jong, W., and Gray, S. (2017) "Mapping Loci That Control Tuber and Foliar Symptoms Caused by PVY in Autotetraploid Potato (Solanum tuberosum L.)". G3 7(11): 3587-3595.
|
|
Related
Code
|
Clark, L.V. "polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids". R package archived at Zenodo.
|
|
Related
Code
|
Blischak, P. "SNP genotyping in polyploids". Software archived at Zenodo.
|
|
Related
Article
|
Hamilton, J. P., Hansey, C. N., Whitty, B. R., Stoffel, K., Massa, A. N., Van Deynze, A., De Jong, W. S., Douches, D. S., Buell, C. R (2011) "Single nucleotide polymorphism discovery in elite north american potato germplasm" BMC Genomics 12:302.
|
|
Related
Code
|
Gerard, D. "updog: Using Parental Data for Offspring Genotyping." Software archived at Zenodo.
|
|
Related
Code
|
Voorrips, R.E. and Gort, G. "fitPoly: Genotype Calling for Bi-Allelic Marker Assays." R Package on CRAN.
|
|
Related
Code
|
Endelman, J. "rrBLUP: Ridge Regression and Other Kernels for Genomic Selection." R Package on CRAN.
|
|
Related
Code
|
Money, D. "LinkImpute: fast and accurate genotype imputation for non-model organisms."
|
|
Related
Dataset
|
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.
|
|
Dataset Description
|
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.
|
|
Subject
|
Life Sciences
|
|
Keywords
|
R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
|
|
License
|
CC BY
|
|
Funder
|
U.S. National Science Foundation (NSF)
-
Grant:
1661490
|
|
Corresponding Creator
|
Lindsay V. Clark
|
|
Downloaded
|
147 times
|
