N90 Contig Length Ninety-Percent Coverage Calculator
Compute N90/L90 from complete positive contig lengths using at-least-90-percent cumulative assembly coverage; no reference genome size assumption.
Description
Compute N90/L90 from complete positive contig lengths using at-least-90-percent cumulative assembly coverage; no reference genome size assumption.
N90 is the contig length at which descending lengths cumulatively account for at least ninety percent of the supplied bases. L90 records how many contigs were needed to reach it.
When to use this tool
Compute N90/L90 from complete positive contig lengths using at-least-90-percent cumulative assembly coverage; no reference genome size assumption.
- Prepare the supplied contigLengths 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. 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.n90, result.l90, result.totalBases. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Require nonempty positive integer lengths and a safe-integer total. Sort descending, accumulate until at least 0.9*totalBases, and return the last length as n90, the number accumulated as l90 and the total.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| contigLengths | contig lengths. | List of finite numbers; bounded by the operation |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.n90 | The n90 value under the stated formula or text convention. |
| result.l90 | The l90 value under the stated formula or text convention. |
| result.totalBases | The total bases value under the stated formula or text convention. |
{
"input": {
"contigLengths": [
5,
3,
2
]
},
"output": {
"result": {
"n90": 2,
"l90": 3,
"totalBases": 10
}
}
}Limitations and assumptions
- The denominator is the supplied assembly total, not an independently known genome size. No gap correction, sequence validation or assembly-quality conclusion is included; ties follow the sorted list.
- 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
- Mean Contig Length Arithmetic Averager
Calculate the arithmetic mean of supplied positive contig lengths.
- Median Contig Length Positional Finder
Calculate the median of supplied positive contig lengths using interpolation between the middle values.