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

Underutilized sheep and goat breeds have the ability to adapt to challenging environments due to their genetic composition. Integrating publicly available genomic datasets with new data will facilitate genetic diversity analyses, however this process is complicated by the fact that data could refer to outdated assembly versions or encoded in different formats. Here we present the SMARTER-database, a collection of tools and scripts to standardize genomic data and metadata on global small ruminant populations with a focus on reproducibility. It harmonizes genotypes for about 12,000 sheep and 6,000 goats to a uniform coding and assembly version. Users can access this data via FTP and interact with it through a REST API, a web interface, or a custom R-package, enabling efficient filtering and selection of samples. These tools will empower researchers to focus on the crucial aspect of adaptation, leveraging the rich dataset provided by the SMARTER-database. Datasets is composed by all samples imported with SMARTER project. However there are additional metadata that could be used to subset the dataset according user's need. Those data are made available to SMARTER Data Portal and SMARTER API. Samples IDs and breed code available through these interface are the same used in the genoypes dataset and could be used to subset data accordinag user needs.