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analyses; however, this process is complicated by data discrepancies, such as outdated assembly
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.
Availability and implementation: The code is available as open-source software under the MIT
license at https://github.com/cnr-ibba/SMARTER-database

Keywords

Animal and Plant Sciences; Bioinformatics; Animal Genetics

Published in

Gigabyte
2024, volume: 2024, article number: 139

SLU Authors

• Johansson, Anna Maria

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Bioinformatics (Computational Biology)
Genetics and Breeding

Publication identifier

• DOI: https://doi.org/10.46471/gigabyte.139

Permanent link to this page (URI)

https://res.slu.se/id/publ/139841