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primerdesigner

Design primers for LIC cloning, Gibson/HiFi assembly, and sequencing from NCBI accessions or raw sequences.

27|4|Updated Feb 8, 2026
Search Tags:#cloning#sequencing#primer-design#lic-primers#gibson-assembly#hifi#orf-verification
One-click install
npx skills add https://github.com/farnunglab/benchaid --skill primerdesigner
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: primerdesigner
Source: https://github.com/farnunglab/benchaid/tree/main/skills/primerdesigner
Command: npx skills add https://github.com/farnunglab/benchaid --skill primerdesigner

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve?

Designing primers for LIC cloning, sequencing, and Gibson/HiFi assembly can be time-consuming and error-prone; this Skill streamlines primer design with a focused CLI workflow.

Core Features & Use Cases

  • LIC cloning primers via Primer3
  • HiFi/Gibson assembly primers
  • ORF verification and sequence validation
  • Vector-ready primer design for common constructs

Quick Start

Run the Primer CLI with an accession or sequence to generate primer sets for LIC cloning, Gibson/HiFi assembly, or sequencing.

Frequently Asked Questions about primerdesigner

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
What primer design methods are available for Gibson assembly and HiFi cloning?▼

The Skill generates LIC cloning primers via Primer3, HiFi/Gibson assembly primers, and sequencing primers for ORF verification. It accepts NCBI accessions or raw sequences to produce vector-ready primer sets.

Does the primer CLI support custom overlap melting temperatures for Gibson assembly?▼

Yes, you can use raw DNA sequences as input for primer design instead of NCBI accessions. The CLI accepts sequence input directly, allowing you to generate primers for LIC tagging, vector assembly, and ORF verification.

What is the difference between lic-only and seq-only primer output modes?▼

You can list available LIC tags and vectors by using the list-lic-tags and list-vectors CLI options. These commands display the predefined tagging and vector constructs compatible with the primer design workflow.

Are there limitations when designing sequencing primers for ORF verification?▼

Specific overlap melting temperatures are needed for HiFi Gibson assembly primers to ensure proper fragment annealing during recombination. The CLI provides an overlap-tm option to customize this parameter for accurate vector assembly.

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