K-mer Frequency Table

Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.

Description

K-mers are overlapping DNA words of a fixed length.

K-mers are overlapping DNA words of a fixed length. Canonicalization can combine a word with its reverse complement into one counting key.

Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.

When to use K-mer Frequency Table

Use this for the following task: Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.

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

How to use K-mer Frequency Table 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 sequence, k, canonicalReverseComplement using the field table, then run the tool.
Read kmers, occurrenceCounts, totalWindows. 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
sequence	Sequence	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]+\s$	Required
k	K	integer; minimum 1	Required
canonicalReverseComplement	Canonical reverse complement	boolean	Required

Normalize canonical DNA and require k to fit. Scan every one-base-offset window, tally keys and sort returned keys lexically with aligned counts.^[1]

totalWindows = sequenceLength−k+1; key = lexical min(kmer,reverseComplement) when enabled

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

Output field	Meaning	Value type
kmers	K-mers	list of string
occurrenceCounts	Occurrence counts	list of integer
totalWindows	Total windows	integer

json

{
  "input": {
    "sequence": "ACAC",
    "k": 2,
    "canonicalReverseComplement": false
  },
  "output": {
    "kmers": [
      "AC",
      "CA"
    ],
    "occurrenceCounts": [
      2,
      1
    ],
    "totalWindows": 3
  }
}

Limitations and assumptions

Window and comparison budgets apply. This does not count across multiple sequences or build a whole-genome spectrum.

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 K-mer Genome Size for this operation: Estimate genome size from retained k-mer occurrences divided by the caller-selected single-copy peak. For a complementary task, use Sliding GC Content for this operation: Calculate GC content in complete DNA windows at a chosen step size.

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

References

K-mer Frequency Table — tool.io

Similar or alternative tools

K-mer Genome Size
Estimate genome size from retained k-mer occurrences divided by the caller-selected single-copy peak.
Sliding GC Content
Calculate GC content in complete DNA windows at a chosen step size.