Number of Contigs Counter with Min-Length Filter
Count supplied contigs passing an inclusive minimum-length filter; no sequence parsing or hidden length inference.
Description
Count supplied contigs passing an inclusive minimum-length filter; no sequence parsing or hidden length inference.
A minimum-length screen divides a supplied contig set into retained and excluded counts. Exact boundary inclusion makes the count reproducible.
When to use this tool
Count supplied contigs passing an inclusive minimum-length filter; no sequence parsing or hidden length inference.
- Prepare the supplied contigLengths, minimumLength fields for this operation.
- Compare the complete example with the representation used by your own input before carrying the result into another step.
How to use the tool and how it works
- Enter contigLengths, minimumLength. Use the exact text syntax, units and index conventions explained below.
- Run the tool. If input validation fails, correct the supplied fields before interpreting any result.
- Read result.atOrAboveMinimum, result.excludedCount. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Validate nonnegative bounded integer minimumLength and contigLengths. Count entries at or above the minimum and entries strictly below it.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| contigLengths | contig lengths. | List of finite numbers; bounded by the operation |
| minimumLength | minimum length. | Integer from 0 to 1e12 inclusive |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.atOrAboveMinimum | The at or above minimum value under the stated formula or text convention. |
| result.excludedCount | The excluded count value under the stated formula or text convention. |
{
"input": {
"contigLengths": [
1,
3,
5
],
"minimumLength": 3
},
"output": {
"result": {
"atOrAboveMinimum": 2,
"excludedCount": 1
}
}
}Limitations and assumptions
- The tool returns counts rather than lengths, IDs or filtered sequences. Zero lengths are allowed and pass a zero minimum; no biological quality or completeness criterion is inferred.
- Every declared top-level field is required and unexpected fields are rejected. Numeric inputs must be finite; ordinary text fields are bounded to 8,192 UTF-16 code units, with tighter operation-specific limits where stated.
- Ordinary string lists have at most 128 entries of at most 128 code units each; numeric lists and matrices have separate bounded size checks. Nonfinite results and excessively large serialized outputs are rejected.
- Indexes are zero-based and spans have an exclusive end unless explicitly stated otherwise. A valid false, null or empty-list result is distinct from malformed input.
Alternative or Complementary methods
Retain the reference assembly, accession/version and measurement convention with an analysis. Length summaries, flags and lookup notes do not validate an assembly or classify a variant; use the corresponding sequence, alignment or evidence-review workflow.
References
Similar or alternative tools
- mapq filter fraction
SAM mapping quality describes confidence in the assigned mapping.
- Mean Contig Length Arithmetic Averager
Calculate the arithmetic mean of supplied positive contig lengths.