EasyKASP: a simple and fast tool for KASP primer design

Abstract

Background: Kompetitive Allele-Specific PCR (KASP) is a fluorescence-based, high-throughput and cost-effective genotyping technology widely used for detecting single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) across various species. However, few software tools are available for automatically designing KASP primers, especially for InDel variations. Results: To address the lack of free and user-friendly automated tools for KASP primer design, we analyzed the sequence characteristics of KASP primers and developed a user-friendly program named EasyKASP on the Excel VBA platform. EasyKASP designs KASP primers for both SNP and InDel variations, with an average processing time of only 0.03 s per primer pair. A total of 80 SNP loci and 6 InDel loci with variations of different lengths were selected to validate the KASP markers designed by EasyKASP, all of which were successfully amplified and genotyped using KASP technology. Conclusions: EasyKASP is a simple and rapid tool for KASP primer design, demonstrating broad applicability in KASP genotyping studies.