The Soybean Allele Catalog Tool: A Web-Based Interactive Tool for Gene Alleles Discovery

The advancement of sequencing technologies has made a plethora of whole genome sequenced (WGS) data publicly available. However, utilizing the raw WGS data will not generate promising research outcomes for agriculture. To solve this problem, the Soybean Allele Catalog Tool ( has been developed to assist researchers in gaining insights into soybean genotypes associated with phenotypes and selecting accessions based on comprehensive soybean SNPs and InDels data organized into alleles of genes. A variant calling pipeline (SnakyVC, and an Allele Catalog pipeline (AlleleCatalog, were developed to prepare the datasets for the tool. The variant calling pipeline processes raw sequencing reads to generate the Variant Call Format (VCF) files in a parallel fashion. Furthermore, the Allele Catalog pipeline can take the VCF files to perform imputations, functional effect predictions, and generate Allele Catalog datasets. Both pipelines were utilized to generate the Soy775 and Soy1066 data panels, consisting of accessions from the Glycine soja and Glycine max from various sources. The Soybean Allele Catalog Tool is a web-based tool that is publicly available for all users via the SoyKB website ( The tool facilitates Allele Catalog data search by genes and accession, visualization, and download capabilities. Utilizing the Soybean Allele Catalog Tool, researchers can acquire a comprehensive understanding of soybean genotypic differences that can contribute to the soybean traits, identify novel alleles of targeted genes, and utilize it in breeding strategies.

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