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Benchmarking database systems for Genomic Selection implementation
- Source :
- Database, Database: The Journal of Biological Databases and Curation
- Publication Year :
- 2019
-
Abstract
- MotivationWith high-throughput genotyping systems now available, it has become feasible to fully integration genotyping information into breeding programs [22]. 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.ResultsWe found that data extract times are greatly influenced by the orientation in which genotype data is stored in a system. HDF5 consistently performed best, in part because it can more efficiently work with both orientations of the allele matrix.Availabilityhttp://gobiinx1.bti.cornell.edu:6083/projects/GBM/repos/benchmarking/browseContactyn259@cornell.edu
- Subjects :
- Genotype
Genotyping Techniques
Computer science
Information Storage and Retrieval
02 engineering and technology
Review
Hierarchical Data Format
computer.software_genre
Logiciel
Turnaround time
General Biochemistry, Genetics and Molecular Biology
F30 - Génétique et amélioration des plantes
Set (abstract data type)
03 medical and health sciences
Relational database management system
020204 information systems
Databases, Genetic
0202 electrical engineering, electronic engineering, information engineering
Information system
Allele
Genotyping
Selection (genetic algorithm)
030304 developmental biology
amélioration génétique
0303 health sciences
Database
U10 - Informatique, mathématiques et statistiques
computer.file_format
Benchmarking
Genomics
L10 - Génétique et amélioration des animaux
DNA extraction
C30 - Documentation et information
General Agricultural and Biological Sciences
Banque de données
computer
Genomic selection
Software
Génotype
Information Systems
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Database, Database: The Journal of Biological Databases and Curation
- Accession number :
- edsair.doi.dedup.....8aa6c8ba2d59c99c873191c293fb58ca