Trailing Adapter Contamination

Detect read-terminal matches to an adapter prefix above the chosen minimum match length.

Description

Adapter contamination can leave a read ending with the start of an adapter sequence.

Adapter contamination can leave a read ending with the start of an adapter sequence. An exact terminal-prefix match provides one specific contamination screen.

Detect read-terminal matches to an adapter prefix above the chosen minimum match length.

When to use Trailing Adapter Contamination

Use this for the following task: Detect read-terminal matches to an adapter prefix above the chosen minimum match length.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Trailing Adapter Contamination and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter readSequences, adapterSequence, minimumMatchBases using the field table, then run the tool.
Read contaminatedReadIndexes, trailingAdapterBases, contaminatedReadPercent. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
readSequences	Canonical DNA reads, limited with the adapter to 10000000 input characters.	list of string; minimum entries 1; maximum entries 100000; each entry: string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]+\s$	Required
adapterSequence	Adapter sequence	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]+\s$	Required
minimumMatchBases	Minimum match bases	integer; minimum 1	Required

Normalize sequences and adapter to uppercase with outer trimming. Build adapter prefix failure links and scan each read in linear time, returning zero-based contaminated indices, match lengths and percent.^[1]

trailing length = longest read suffix matching adapter prefix, if length ≥ minimum

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
contaminatedReadIndexes	Contaminated read indexes	list of integer
trailingAdapterBases	Trailing adapter bases	list of integer
contaminatedReadPercent	Contaminated read percent	number

json

{
  "input": {
    "readSequences": [
      "ACGTAAA",
      "ACGT"
    ],
    "adapterSequence": "AAA",
    "minimumMatchBases": 3
  },
  "output": {
    "contaminatedReadIndexes": [
      0
    ],
    "trailingAdapterBases": [
      3,
      0
    ],
    "contaminatedReadPercent": 50
  }
}

Limitations and assumptions

Internal adapters, mismatches and reverse-complement adapters are not detected. Input characters are bounded and the minimum cannot exceed adapter length.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Overrepresented Read Screen for this operation: Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling. For a complementary task, use K-mer Frequency Table for this operation: Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Trailing Adapter Contamination — tool.io

Similar or alternative tools

Overrepresented Read Screen
Flag exact-sequence read abundance fractions above a caller-defined overrepresentation ceiling.
K-mer Frequency Table
Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.