SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds

[EN] 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data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versio...

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Detalles Bibliográficos
Autores: Cozzi, Paolo, Manunza, Arianna, Ramírez Díaz, Johanna, Tsartsianidou, Valentina, Gkagkavouzis, Konstantinos, Peraza, Pablo, Johansson, Anna Maria, Arranz Santos, Juan José, Freire, Fernando, Kusza, Szilvia, Biscarini, Filippo, Peters, Lucy, Tosser-Klopp, Gwenola, Ciappesoni, Gabriel, Triantafyllidis, Alexandros, Rupp, Rachel, Servin, Bertrand, Stella, Alessandra
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Universidad de León
Repositorio:BULERIA. Repositorio Institucional de la Universidad de León
OAI Identifier:oai:buleria.unileon.es:10612/24290
Acceso en línea:https://gigabytejournal.com/articles/139
https://hdl.handle.net/10612/24290
Access Level:acceso abierto
Palabra clave:Producción animal
Veterinaria
Animal and Plant Sciences
Bioinformatics
Animal Genetics
3109 Ciencias Veterinarias
3104 Producción Animal
Descripción
Sumario:[EN] 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data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats.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

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