Hooksnip: A Browser Tool for Designing Allele-Specific PCR Primers in Hookworm

Surveillance for anthelmintic resistance in hookworms requires low-cost, field-deployable genotyping strategies. Allele-specific PCR (AS-PCR) is attractive because it discriminates single-nucleotide polymorphisms (SNPs) at the 3' end of a primer without sequencing infrastructure, thereby enabling rapid detection of drug-resistance markers directly from eggs or larvae. Here, we present hookSNiP (https://ohalloranlab.net/hooksnip), a browser-based application that designs allele-specific primer pairs for Ancylostoma species. The tool provides curated reference genomes, validation of variant call format (VCFs) and genome sequence compatibility, strand-aware primer orientation using gene annotations, and tiered rescue modes when strict primer design constraints cannot be met. By combining these features with AS-PCR, hookSNiP reduces practical barriers to SNP validation and expands the feasibility of large-scale resistance monitoring.