EasyKASP: a simple and fast tool for KASP primer designing

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