@article {nti-addae_benchmarking_2019,
	title = {Benchmarking Database Systems for Genomic Selection Implementation},
	year = {Submitted},
	pages = {baz096},
	abstract = {Motivation: With high-throughput genotyping systems now available, it has become feasible to fully integration genotyping information into breeding programs. To make use of this information effectively requires {DNA} extraction facilities and marker production facilities that can efficiently deploy the desired set of markers across samples with a rapid turnaround time that allows for selection before crosses needed to be made. In reality, breeders often have a short window of time to make decisions by the time they are able collect all their phenotyping data and receive corresponding genotyping data. This presents a challenge to organize information and utilize them in downstream analyses to support decisions made by breeders. In order to implement genomic selection routinely as part of breeding programs one would need an efficient genotype data storage system. We selected and benchmarked six popular open-source data storage systems, including relational database management and columnar storage systems. Results: We found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. {HDF}5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.},
	doi = {10.1093/database/baz096},
	url = {http://doi.org/10.1093/database/baz096},
	author = {Nti-Addae, Yaw and Matthews, Dave and Ulat, Victor Jun and Syed, Raza and Sempere, Guilhem and Petel, Adrien and Renner, Jon and Larmande, Pierre and Guignon, Valentin and Jones, Elizabeth and Robbins, Kelly}
}
