Quickstart

Quick Start

Design your first PCR primers in 5 minutes.

Step 1: Verify Installation

primerlab health

You should see:

✅ Primer3 core found
✅ Python 3.10+
⚠️ BLAST+ not found (optional)
⚠️ ViennaRNA not found (optional)

Note: BLAST+ and ViennaRNA are optional. You can still design primers without them.

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Step 2: Create Configuration

Create a file called my_first_design.yaml:

# my_first_design.yaml
input:
  sequence: >
    ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGAC
    GGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTAC
    GGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACC
    CTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAG
    CAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTC
    TTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTG
    GTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCAC

parameters:
  tm:
    opt: 60.0
  product_size:
    min: 150
    max: 300

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Step 3: Run Design

primerlab run pcr --config my_first_design.yaml

Expected output:

🧬 PrimerLab PCR Design
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
✅ 5 primer pairs designed

Pair 1 (Score: 92.5)
  Forward: ATGGTGAGCAAGGGCGAGGAG (Tm: 60.2°C)
  Reverse: CCCAGGCATCCTTGAAGAA (Tm: 59.8°C)
  Product: 245 bp

📁 Output: primerlab_output/

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Step 4: Review Results

Check the output directory:

ls primerlab_output/

Files generated:

• primers.json — Machine-readable results
• report.md — Human-readable report
• primers_idt.csv — Ready for IDT ordering

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Next Steps

• Full PCR Tutorial — Learn all PCR options
• qPCR Design — Design TaqMan probes
• CLI Reference — All command options

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Common Issues

“Primer3 not found”

# Install via conda
conda install -c bioconda primer3

# Or build from source
# See: https://github.com/primer3-org/primer3

“No primers found”

• Your sequence may be too short (min ~100 bp recommended)
• Try relaxing constraints (lower min Tm, larger product range)