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

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data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly...

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Detalles Bibliográficos
Autores: COZZI, P., MANUNZA, A., RAMIREZ-DIAZ, J., TSARTSIANIDOU, V., GKAGKAVOUZIS, K., PERAZA, P., JOHANSSON, A. M., ARRANZ, J. J., FREIRE, F., KUSZA, S., BISCARINI, F., PETERS, L., TOSSER-KLOPP, G., CIAPPESONI, G., TRIANTAFYLLIDIS, A., RUPP, R., SERVIN, B., STELLA, A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:Uruguay
Institución:Instituto Nacional de Investigación Agropecuaria
Repositorio:AINFO
Idioma:inglés
OAI Identifier:oai:redi.anii.org.uy:20.500.12381/4950
Acceso en línea:https://ainfo.inia.uy/consulta/busca?b=pc&id=64970&biblioteca=vazio&busca=64970&qFacets=64970
Access Level:acceso abierto
Palabra clave:Animal and Plant Sciences
Bioinformatics
Animal Genetics
SISTEMA GANADERO EXTENSIVO - INIA
SMARTER-database
Descripción
Sumario: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data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats.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. © 2024 GigaScience Press. All rights reserved. .-.-.-.-.-.-.-.-.-. Availability and implementation:The code is available as open-source software under the MIT license at https://github.com/cnr-ibba/SMARTER-database.

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