K-mer Genome Size
Estimate genome size from retained k-mer occurrences divided by the caller-selected single-copy peak.
Description
A k-mer spectrum relates retained occurrence mass to its chosen single-copy depth peak.
A k-mer spectrum relates retained occurrence mass to its chosen single-copy depth peak. Their quotient gives a simplified genome-size estimate.
Estimate genome size from retained k-mer occurrences divided by the caller-selected single-copy peak.
When to use K-mer Genome Size
Use this for the following task: Estimate genome size from retained k-mer occurrences divided by the caller-selected single-copy peak.
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 Genome Size 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 kmerOccurrences, lowCountErrorOccurrences, mainPeakDepth using the field table, then run the tool.
- Read retainedOccurrences, estimatedGenomeBases. 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 |
|---|---|---|---|
| kmerOccurrences | Kmer occurrences | integer; minimum 0 | Required |
| lowCountErrorOccurrences | Low count error occurrences | integer; minimum 0 | Required |
| mainPeakDepth | Main peak depth | number; greater than 0 | Required |
Require nonnegative counts with errors no greater than total and a positive peak depth. Divide retained mass by the caller-selected peak.1
retained = totalOccurrences − lowCountErrorOccurrences; size = retained/mainPeakDepth This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| retainedOccurrences | Retained occurrences | integer |
| estimatedGenomeBases | Estimated genome bases | number |
{
"input": {
"kmerOccurrences": 1000000,
"lowCountErrorOccurrences": 100000,
"mainPeakDepth": 30
},
"output": {
"retainedOccurrences": 900000,
"estimatedGenomeBases": 30000
}
}Limitations and assumptions
Peak selection and error classification are inputs. Heterozygosity, repetitive peaks and end corrections are not modeled.
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 Frequency Table for this operation: Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization. For a complementary task, use Sequencing Fold Depth for this operation: Compute theoretical sequencing depth from individual read count, read length, and genome size.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
K-mer Genome Size — tool.io
Similar or alternative tools
- K-mer Frequency Table
Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.
- Sequencing Fold Depth
Compute theoretical sequencing depth from individual read count, read length, and genome size.