Quick Start Tutorial

Tutorial: Quick Start Tutorial

Design your first PCR primers in 5 minutes.

Step 1: Prepare Your Sequence

Save your target sequence as my_gene.fasta:

>My_Target_Gene
ATGAGTAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGT
GATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGA
AAACTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTT
GTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGG
CATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTC
AAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTT
AATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAA
CTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGA
ATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGAC
CATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTAC

---

Step 2: Create Configuration

Create pcr_config.yaml:

workflow: pcr

input:
  sequence_path: "my_gene.fasta"

parameters:
  primer_size: {min: 18, opt: 20, max: 24}
  tm: {min: 58.0, opt: 60.0, max: 62.0}
  product_size_range: [[200, 400]]

output:
  directory: "output_pcr"

---

Step 3: Run Primer Design

primerlab run pcr --config pcr_config.yaml

Expected output:

🧬 PrimerLab v0.3.5
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
[1/5] Loading sequence...
[2/5] Designing primers...
[3/5] Running QC...
[4/5] Scoring primers...
[5/5] Generating report...

✅ Design complete!
   Primers: 5 pairs
   Best score: 95.2
   Output: output_pcr/

---

Step 4: View Results

Check the report

cat output_pcr/report.md

View primer details

cat output_pcr/result.json | jq '.primers[0]'

Example output:

{
  "forward": {
    "sequence": "ATGAGTAAAGGAGAAGAACT",
    "tm": 58.5,
    "gc": 40.0,
    "length": 20
  },
  "reverse": {
    "sequence": "GCCGTGATGTATACATTGTG",
    "tm": 59.2,
    "gc": 45.0,
    "length": 20
  },
  "amplicon_size": 320,
  "score": 95.2
}

---

Step 5: Validate (Optional)

Run in-silico PCR to validate:

primerlab insilico \
  -f "ATGAGTAAAGGAGAAGAACT" \
  -r "GCCGTGATGTATACATTGTG" \
  -t my_gene.fasta

---

Next Steps

• PCR Walkthrough - Detailed configuration
• qPCR Design - TaqMan assay design
• Off-target Analysis - BLAST check

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Troubleshooting

Issue	Solution
No primers found	Relax Tm or product size range
File not found	Check file path
Invalid sequence	Ensure FASTA format

See Troubleshooting for more.