primerlab amplicon-qc

CLI reference for the primerlab amplicon-qc command

Validate qPCR amplicon quality and characteristics (v0.6.0).

Usage

primerlab amplicon-qc --amplicon <SEQUENCE> [OPTIONS]

Arguments

Argument	Required	Description
--amplicon, -a	Yes	Amplicon sequence or FASTA file path
--min-length	No	Minimum length (default: 70 bp)
--max-length	No	Maximum length (default: 150 bp)
--output, -o	No	Output file path
--format	No	Output format: text or json

Examples

Basic amplicon QC

primerlab amplicon-qc --amplicon ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG

Output:

═══════════════════════════════════════════════════════
                   AMPLICON QC (v0.6.0)
═══════════════════════════════════════════════════════
Length:           97 bp
GC Content:       50.5%
Amplicon Tm:      73.7°C

Validation:
  Length OK:      ✅
  GC OK:          ✅
  Structure OK:   ✅

Quality Score:    95/100
Grade:            A

Custom length range

primerlab amplicon-qc \
  --amplicon ATGCGATCGATCGATCGATCG \
  --min-length 50 \
  --max-length 200

From FASTA file

primerlab amplicon-qc --amplicon amplicon.fasta

JSON output

primerlab amplicon-qc --amplicon ATGCGATCGATCGATCGATCG --format json -o result.json

Validation Criteria

Criterion	Optimal Range	Description
Length	70-150 bp	qPCR optimal amplicon size
GC Content	40-60%	Balanced base composition
Secondary Structure	ΔG > -3 kcal/mol	Minimal self-folding

Output Fields

Field	Description
Length	Amplicon length in bp
GC Content	Percentage of G+C bases
Amplicon Tm	Predicted melting temperature
Length OK	Passes length validation
GC OK	Passes GC content validation
Structure OK	Passes secondary structure check
Quality Score	Overall score (0-100)
Grade	Quality grade (A-F)

See Also

• probe-check - TaqMan probe binding
• melt-curve - SYBR melt curve prediction
• qPCR Advanced Tutorial