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SMARTER数据库：一种整合绵羊和山羊品种SNP阵列数据集的工具。

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

作者信息

Cozzi Paolo, Manunza Arianna, Ramirez-Diaz Johanna, Tsartsianidou Valentina, Gkagkavouzis Konstantinos, Peraza Pablo, Johansson Anna Maria, Arranz Juan José, Freire Fernando, Kusza Szilvia, Biscarini Filippo, Peters Lucy, Tosser-Klopp Gwenola, Ciappesoni Gabriel, Triantafyllidis Alexandros, Rupp Rachel, Servin Bertrand, Stella Alessandra

机构信息

Institute of Agricultural Biology and Biotechnology, National Research Council, Via Alfonso Corti nr. 12, 20133, Milano, Italy.

Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece.

出版信息

GigaByte. 2024 Oct 21;2024:gigabyte139. doi: 10.46471/gigabyte.139. eCollection 2024.

DOI:10.46471/gigabyte.139
PMID:39473492
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11519891/
Abstract

UNLABELLED

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data will facilitate genetic diversity analyses; however, this process is complicated by data discrepancies, such as outdated assembly versions or different data formats.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

摘要

未标注

未得到充分利用的绵羊和山羊品种因其遗传特性能够适应具有挑战性的环境。将公开可用的基因组数据集与新数据整合将有助于进行遗传多样性分析；然而，这一过程因数据差异而变得复杂，如组装版本过时或数据格式不同。在此，我们展示了SMARTER数据库，这是一个工具和脚本集合，用于标准化基因组数据和元数据，主要来自全球小型反刍动物群体的SNP芯片阵列，重点在于可重复性。SMARTER数据库将约12000只绵羊和6000只山羊的基因型统一到一个一致的编码和组装版本。用户可以通过文件传输协议访问基因型数据，并通过网络界面或使用自定义脚本与元数据进行交互，从而实现对样本的高效筛选和选择。这些工具将使研究人员能够专注于适应的关键方面，并利用SMARTER数据库提供的丰富数据集为牲畜的可持续发展做出贡献。

可用性和实施

代码以开源软件形式提供，遵循MIT许可，可在https://github.com/cnr-ibba/SMARTER-database获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/d635260bac82/gigabyte-2024-139-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/a2525f8cb973/gigabyte-2024-139-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/73dbedd98c34/gigabyte-2024-139-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/e0abc7819cf1/gigabyte-2024-139-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/c7130ee450ac/gigabyte-2024-139-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/62a3ff9e55b7/gigabyte-2024-139-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/d635260bac82/gigabyte-2024-139-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/a2525f8cb973/gigabyte-2024-139-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/73dbedd98c34/gigabyte-2024-139-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/e0abc7819cf1/gigabyte-2024-139-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5262/11519891/c7130ee450ac/gigabyte-2024-139-g004.jpg
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