The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis
Abstract Background The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-03-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09161-3 |
| _version_ | 1827985149006970880 |
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| author | Yen On Chan Nicholas Dietz Shuai Zeng Juexin Wang Sherry Flint-Garcia M. Nancy Salazar-Vidal Mária Škrabišová Kristin Bilyeu Trupti Joshi |
| author_facet | Yen On Chan Nicholas Dietz Shuai Zeng Juexin Wang Sherry Flint-Garcia M. Nancy Salazar-Vidal Mária Škrabišová Kristin Bilyeu Trupti Joshi |
| author_sort | Yen On Chan |
| collection | DOAJ |
| description | Abstract Background The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. Results The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. Conclusions The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species. |
| first_indexed | 2024-04-09T23:09:15Z |
| format | Article |
| id | doaj.art-eb6165b8c7424b629d9f9f139fc1cc11 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:09:15Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-eb6165b8c7424b629d9f9f139fc1cc112023-03-22T10:30:58ZengBMCBMC Genomics1471-21642023-03-0124111410.1186/s12864-023-09161-3The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysisYen On Chan0Nicholas Dietz1Shuai Zeng2Juexin Wang3Sherry Flint-Garcia4M. Nancy Salazar-Vidal5Mária Škrabišová6Kristin Bilyeu7Trupti Joshi8MU Institute for Data Science and Informatics, University of Missouri-ColumbiaDivision of Plant Science and Technology, University of Missouri-ColumbiaDepartment of Electrical Engineering and Computer Science, University of Missouri-ColumbiaChristopher S. Bond Life Sciences Center, University of Missouri-ColumbiaUnited States Department of Agriculture-Agricultural Research Service, Plant Genetics Research UnitDivision of Plant Science and Technology, University of Missouri-ColumbiaDepartment of Biochemistry, Faculty of Science, Palacky University in OlomoucUnited States Department of Agriculture-Agricultural Research Service, Plant Genetics Research UnitMU Institute for Data Science and Informatics, University of Missouri-ColumbiaAbstract Background The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. Results The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. Conclusions The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.https://doi.org/10.1186/s12864-023-09161-3Variant Calling PipelineAllele Catalog PipelineAllele Catalog ToolAlleles in GeneData Visualization |
| spellingShingle | Yen On Chan Nicholas Dietz Shuai Zeng Juexin Wang Sherry Flint-Garcia M. Nancy Salazar-Vidal Mária Škrabišová Kristin Bilyeu Trupti Joshi The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis BMC Genomics Variant Calling Pipeline Allele Catalog Pipeline Allele Catalog Tool Alleles in Gene Data Visualization |
| title | The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis |
| title_full | The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis |
| title_fullStr | The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis |
| title_full_unstemmed | The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis |
| title_short | The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis |
| title_sort | allele catalog tool a web based interactive tool for allele discovery and analysis |
| topic | Variant Calling Pipeline Allele Catalog Pipeline Allele Catalog Tool Alleles in Gene Data Visualization |
| url | https://doi.org/10.1186/s12864-023-09161-3 |
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