primerXL

primerXL designs high-quality singleplex PCR assays for targeted resequencing, maximizing target coverage and providing uniform coverage across target regions.

Key Features:

• Optimized cascade of relaxed design criteria: Employs a cascade of progressively relaxed primer design constraints to generate high-quality singleplex PCR assays and reduce the need for amplicon normalization.
• In silico evaluation process: Performs comprehensive in silico evaluation of primer specificity and assay quality.
• Coverage uniformity and flexibility: Produces uniform coverage across target regions and supports customization of design parameters and workflows.
• High target coverage via overlapping assays: Generates partially overlapping assays to maximize target coverage and is reported to outperform other target enrichment strategies and similar primer design tools.

Scientific Applications:

• Targeted resequencing: Design and evaluation of PCR assays for targeted resequencing projects, demonstrated across four projects producing 2,348 amplicons covering 470 kb.

Methodology:

Uses an optimized cascade of relaxed design criteria, a comprehensive in silico evaluation process, and generation of partially overlapping singleplex PCR assays within a customizable workflow.