primerlab multiplex

CLI reference for the primerlab multiplex command

Check multiplex compatibility of primer sets (v0.4.0)

Synopsis

primerlab multiplex --primers <file.json> [options]

Description

Analyzes a set of primer pairs for multiplex PCR compatibility by checking cross-dimer formation, Tm uniformity, and GC content consistency.

Required Arguments

Argument	Description
--primers, -p	Path to JSON file containing primer pairs

Optional Arguments

Argument	Default	Description
--config, -c	-	Path to custom YAML config
--output, -o	multiplex_output	Output directory
--format	markdown	Report format (markdown or json)

Examples

Basic Usage

# Analyze primers from JSON file
primerlab multiplex --primers my_primers.json

# Specify output directory
primerlab multiplex --primers primers.json --output results/

# Use custom configuration
primerlab multiplex --primers primers.json --config strict_config.yaml

Input File Format

Create a JSON file with your primer pairs:

[
  {
    "name": "GAPDH",
    "fwd": "ATGGGGAAGGTGAAGGTCGG",
    "rev": "GGATCTCGCTCCTGGAAGATG",
    "tm_fwd": 60.5,
    "tm_rev": 61.2,
    "gc_fwd": 60.0,
    "gc_rev": 57.0
  },
  {
    "name": "ACTB",
    "fwd": "CATGTACGTTGCTATCCAGGC",
    "rev": "CTCCTTAATGTCACGCACGAT"
  }
]

Note: tm_fwd, tm_rev, gc_fwd, gc_rev are optional. If not provided, validation rules that depend on these values may flag warnings.

Output Files

The command generates the following files in the output directory:

File	Description
multiplex_report.md	Human-readable Markdown report
multiplex_analysis.json	Complete analysis in JSON format
multiplex_analysis.xlsx	Excel workbook with matrix (if openpyxl installed)
idt_plate_order.csv	IDT plate format for ordering

Exit Codes

Code	Meaning
0	Analysis complete, primers are compatible
1	Analysis complete, primers have compatibility issues

Integration with run Command

Use --check-multiplex flag with primerlab run to automatically check designed primers:

primerlab run pcr --config design.yaml --check-multiplex

See Also

• Multiplex Feature Guide
• Configuration Reference