Reference haplotypes
Study haplotype
Welcome to AGIDB
Welcome to our all-in-one Imputation Platform (AGIDB), the premier hub for genomic research spanning 89 diverse species. Our platform provides a treasure trove of information, featuring in-depth reference panels, dynamic haplotype visualization, and cutting-edge imputation techniques encompassing four tailored scenarios to meet your specific requirements. Capitalize on our ENCODE-annotated SNP database and delve into our robust toolset, including ImpRefIC, principal component analysis, selective sweep analysis and versatile data format conversions, all meticulously crafted to enhance your research workflow. Embark on your journey through our intuitive interface and unveil groundbreaking insights to propel your research forward. For swine genomic research, we invite you to explore our specialized Pig Imputation Platform (PGIDB) for a more focused experience. Begin your voyage and enrich your research today!
Publication
Kaili Zhang, Jiete Liang, Yuhua Fu, Jinyu Chu, Liangliang Fu, Yongfei Wang, Wangjiao Li, You Zhou, Jinhua Li, Xiaoxiao Yin, Haiyan Wang, Xiaolei Liu, Chunyan Mou, Chonglong Wang, Heng Wang, Xinxing Dong, Dawei Yan, Mei Yu, Shuhong Zhao, Xinyun Li, Yunlong Ma, AGIDB: a versatile database for genotype imputation and variant decoding across species, Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D835–D849, https://doi.org/10.1093/nar/gkad913
Data Statistics
For better visualization, we randomly picked 21 species for display here.
- Total Animals: 35; Genera: 50; Distinct Species: 89
- Samples: 192,305
- Bases: 688.57 TB
- Peaks: 143.10 M
Latest News
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2024/1/5
AGIDB was officially online.
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2023/10/27
AGIDB manuscript was online. Links to the article
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2023/8/6
Updated "Imputation" and "Search" modules.
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2023/7/30
Added selective sweep analysis module.
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2023/6/4
AGIDB and PGIDB were currently in the trial and testing.
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2023/5/4
AGIDB and PGIDB were released to the Internet environment.
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2023/3/9
Update Beagle to the latest version, and update the low-depth sequencing imputation software GLIMPSE1 to GLIMPSE2.
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2023/1/18
The SNP retrieval function is updated, and the SNP annotation is enriched by using the peak information of ENCODE.
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2022/12/2
The genome browser is bound to realize the visualization of genome data.
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2022/10/17
Complete the principal component analysis module and the genome data format conversion module.
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2022/9/23
Development of ImpRefIC, a software that can customize an optimal reference set for genotype imputation to improve imputation accuracy and speed up imputation.
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2022/7/1
Customized SNP retrieval and imputation module for pig, designed pig imputation platform (PGIDB).
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2022/5/20
The software used for low-depth sequencing imputation was determined to be GLIMPSE.
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2022/4/10
Update genotype imputation modules to meet individual imputation needs.
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2022/3/25
Updated WGS data for 35 animals.
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2022/2/15
Complete the imputation module.
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2021/12/28
Determine the imputation software and imputation evaluation scheme, and design the imputation module.
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2021/12/16
Integrate the haplotype analysis results into AGIDB in the form of haplotype modules to realize the retrieval and visualization of haplotype blocks.
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2021/11/8
Complete data cleaning and phasing, and determine the haplotype analysis scheme.
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2021/10/20
Whole-genome sequencing (WGS) data for 35 animals were collated and cleaned.
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2021/6/7
Complete the framework design of Animal Genotype Imputation Database (AGIDB).
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