NTC Contamination Gate

Flag early no-template-control amplification against caller-supplied Ct limits.

Description

A no-template control can show amplification or be encoded by a caller's undetected Ct sentinel.

A no-template control can show amplification or be encoded by a caller's undetected Ct sentinel. The classification depends on both that sentinel and the contamination threshold.^[1]

Flag early no-template-control amplification against caller-supplied Ct limits.

When to use NTC Contamination Gate

Use this tool to flag early no-template-control amplification against caller-supplied Ct limits.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use NTC Contamination Gate and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter noTemplateCt, maximumContaminationCt, undetectedCt using the field table and calculation rules, then run the tool.
Read contaminationFlag, detected, cyclesAfterThreshold. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
noTemplateCt	No template ct	number	Required
maximumContaminationCt	Maximum contamination ct	number	Required
undetectedCt	Undetected ct	number	Required

Provide finite control Ct, positive undetected sentinel and nonnegative contamination cutoff. Return detected status, contamination flag and signed cycles after the cutoff. A Ct equal to the sentinel is undetected even if it meets the contamination cutoff.

detected=Ct<undetectedCt; flag=detected AND Ct≤maximumContaminationCt

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
contaminationFlag	Contamination flag	boolean
detected	Detected	boolean
cyclesAfterThreshold	Cycles after threshold	number

json

{
  "input": {
    "noTemplateCt": 38,
    "maximumContaminationCt": 35,
    "undetectedCt": 45
  },
  "output": {
    "contaminationFlag": false,
    "detected": true,
    "cyclesAfterThreshold": 3
  }
}

Limitations and assumptions

The tool does not analyze amplification curves or establish contamination causality. The two thresholds need not be ordered by validation; signed Ct inputs are accepted.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Melting Peak Specificity: Gate amplicon specificity by significant melting-curve peak count. For a complementary task, use MIQE Coverage Audit: Audit caller-supplied MIQE reporting checklist coverage.

References

NTC Contamination Gate — tool.io

Similar or alternative tools

Melting Peak Specificity
Gate amplicon specificity by significant melting-curve peak count.
MIQE Coverage Audit
Audit caller-supplied MIQE reporting checklist coverage.