Johansson, Anna Maria
- Department of Animal Biosciences, Swedish University of Agricultural Sciences
Research article2024Peer reviewedOpen access
SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds
Cozzi, Paolo; Manunza, Arianna; Ramirez-Diaz, Johanna; Tsartsianidou, Valentina; Gkagkavouzis, Konstantinos; Peraza, Pablo; Johansson, Anna Maria; Arranz, Juan Jose; Freire, Fernando; Kusza, Szilvia; Biscarini, Filippo; Peters, Lucy; Tosser-Klopp, Gwenola; Ciappesoni, Gabriel; Triantafyllidis, Alexandros; Rupp, Rachel; Servin, Bertrand; Stella, Alessandra
Abstract
Underutilized sheep and goat breeds can adapt to challenging environments due to their genetics. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats. Here, we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata, mainly from SNP chip arrays on global small ruminant populations, with a focus on reproducibility. SMARTER-database harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access the genotype data via File Transfer Protocol and interact with the metadata through a web interface or using their custom scripts, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspects of adaptation and contribute to livestock sustainability, leveraging the rich dataset provided by the SMARTER-database.
Keywords
Animal and Plant Sciences; Bioinformatics; Animal Genetics
Published in
Gigabyte
2024, volume: 2024, article number: 139
SLU Authors
UKÄ Subject classification
Bioinformatics (Computational Biology)
Genetics and Breeding in Agricultural Sciences
Publication identifier
- DOI: https://doi.org/10.46471/gigabyte.139
Permanent link to this page (URI)
https://res.slu.se/id/publ/139841