The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis

Area of Science:

• Genomics
• Bioinformatics
• Plant Science

Background:

• Advancements in sequencing technologies have generated vast amounts of publicly available whole-genome re-sequencing (WGRS) data.
• Utilizing WGRS data for research is challenging due to the need for further configuration and specialized tools.
• There is a need for accessible platforms to explore genetic variation within large plant populations.

Purpose of the Study:

• To develop an interactive tool for exploring coding region allelic variation in WGRS data.
• To enable researchers to easily query and analyze genetic variants across multiple plant species.
• To bridge the gap between raw sequencing data and actionable biological insights.

Main Methods:

• Development of two parallelized pipelines: SnakyVC for variant calling and AlleleCatalog for data curation.
• Generation of Variant Call Format (VCF) files and curated Allele Catalog datasets for over 1,000 accessions each of soybean, Arabidopsis, and maize.
• Implementation of data query, visualization, categorical filtering, and download functionalities within a web-based tool.

Main Results:

• The Allele Catalog Tool provides curated datasets with imputed variants, functional effect predictions, and assembled alleles for each gene.
• Users can query genetic variation, view summary results, and access detailed genotypic information including variant positions, genotypes, and predicted functional effects.
• The tool facilitates the connection of variant alleles with specific meta-information for each species, enhancing data interpretability.

Conclusions:

• The Allele Catalog Tool is a web-based resource supporting soybean, Arabidopsis, and maize.
• The tool is accessible via SoyKB (soybean) and KBCommons (Arabidopsis, maize) websites.
• It empowers researchers to effectively link gene variant alleles with species-specific meta-information for further biological discovery.