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title: "primerlab insilico" description: "CLI reference for the primerlab insilico command"

v0.2.4 - In-silico PCR Simulation

Validate primers against a template sequence by simulating PCR amplification.

Usage

primerlab insilico -p <primers> -t <template> [options]

Arguments

Argument Short Required Description
--primers -p ✅ Path to primers file (JSON or FASTA)
--template -t ✅ Path to template FASTA file
--output -o ❌ Output directory (default: insilico_output)
--config -c ❌ Optional config file for parameters
--json ❌ Output results as JSON only
--circular ❌ Treat template as circular (v0.2.4)

Primer File Formats

JSON Format

{
  "forward": "ATGGTGAGCAAGGGCGAGGAG",
  "reverse": "TTACTTGTACAGCTCGTCCATGCC"
}

FASTA Format

>Forward_primer
ATGGTGAGCAAGGGCGAGGAG
>Reverse_primer
TTACTTGTACAGCTCGTCCATGCC

Examples

Basic Usage

primerlab insilico -p primers.json -t template.fasta

With Custom Output Directory

primerlab insilico -p primers.json -t template.fasta -o results/

JSON Output for Pipelines

primerlab insilico -p primers.json -t template.fasta --json > result.json

Using Example Files

primerlab insilico \
  -p examples/insilico/primers.json \
  -t examples/insilico/template.fasta

Output Files

File Description
insilico_result.json Complete results with binding data
insilico_report.md Human-readable markdown report (v0.2.2)
predicted_amplicons.fasta Predicted amplicon sequences

Console Output

============================================================
🧬 In-silico PCR Results
============================================================
Template: GFP_coding_sequence (720 bp)
Forward:  5'-ATGGTGAGCAAGGGCGAGGAG-3' (21 bp)
Reverse:  5'-TTACTTGTACAGCTCGTCCATGCC-3' (24 bp)
------------------------------------------------------------

✅ 1 product(s) predicted

🎯 PRIMARY: 720 bp
   Position: 0 → 720
   Likelihood: 100.0%

   Amplicon: ATGGTGAGCAAGGGCGAGGAG...GGCATGGACGAGCTGTACAAGTAA

------------------------------------------------------------
📁 Output directory: insilico_output
   • insilico_result.json
   • predicted_amplicons.fasta (1 sequences)

What It Checks

  • Primer Binding Sites - Finds all positions where primers can bind
  • 3' End Match - Verifies 3' stability (minimum 3bp perfect match)
  • 5' Mismatch Tolerance - Allows up to 2 mismatches at 5' end
  • Product Size - Validates amplicon is within expected range
  • Multiple Products - Detects potential non-specific amplification
  • Orientation - Ensures primers face each other correctly

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