Genotyping Assay Design

A unified suite of browser-based tools for SNP, InDel and haplotype genotyping — from allele-specific PCR and fluorescent probes to single-base extension and capillary electrophoresis.

Explore Tools Documentation
Typical genotyping workflow
1
Select variant type

Identify SNP, InDel, or haplotype of interest from sequence data.

2
Choose assay platform

Match throughput, equipment, and budget to the right chemistry.

3
Design primers & probes

Use the tools below to generate optimised oligos instantly.

4
Validate & score

Run in silico PCR, check specificity, then genotype your samples.

Genotyping Tools
KASP Genotyping Assay

Design allele-specific primers for KASP™, PACE™, ASQ and generic AS-PCR assays. Supports biallelic SNPs, InDels and complex haplotypes with automatic tail selection and Tm balancing.

AS-PCR KASP™ PACE™ ASQ SNP / InDel Haplotypes
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SNP/InDel Genotyping by qPCR — Dual-Labelled Probes

Design TaqMan, MGB and Molecular Beacon probes for quantitative allelic discrimination. Generates allele-specific probe pairs with matched Tms and minimal cross-reactivity, ready for 5′-nuclease or hairpin-based detection.

TaqMan MGB Probe Molecular Beacon qPCR SNP / InDel
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SNaPshot® Multiplex SNP Genotyping

Design single-base extension (SBE) primers for multiplex SNP and InDel genotyping on capillary electrophoresis platforms (Applied Biosystems SNaPshot®). Also supports BAC fingerprinting and CpG methylation analysis by minisequencing.

SBE Minisequencing Multiplex Capillary CE Methylation BAC Fingerprint
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PCR, Multiplex & QF-PCR Design

General-purpose primer design engine covering standard, inverse, multiplex, TaqMan, MGB-probe, bisulfite and RPA assays. Quantitative fluorescent PCR (QF-PCR) mode generates STR-flanking primers for dosage analysis and CNV genotyping.

Standard PCR Multiplex PCR QF-PCR / STR Bisulfite PCR RPA TaqMan
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Method Comparison
Feature KASP / AS-PCR qPCR Probes SNaPshot SBE QF-PCR / STR
SNP genotyping ✔ ✔ ✔ —
InDel detection ✔ ✔ ✔ ✔
STR / microsatellite — — ± ✔
Multiplex (≥10 loci) ± ± ✔ ✔
Haplotype phasing ✔ — ± —
Methylation analysis — — ✔ —
qPCR instrument required ✔ ✔ — —
Capillary electrophoresis — — ✔ ✔
Low-cost plate reader ✔ — — —
Dosage / CNV analysis — ± — ✔

✔ fully supported   ± partially supported   — not applicable

All computations run locally in your browser. Your sequences are never sent to any server.
© Ruslan Kalendar Documentation →