Assembly N50
Find the contig length at which descending cumulative length reaches half the assembly.
Description
Assembly N50 is a length-weighted contiguity summary.
Assembly N50 is a length-weighted contiguity summary. It is the contig length where descending cumulative assembly length first reaches half the assembly.1
Find the contig length at which descending cumulative length reaches half the assembly.
When to use Assembly N50
Use this for the following task: Find the contig length at which descending cumulative length reaches half the assembly.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Assembly N50 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 contigLengths using the field table, then run the tool.
- Read n50, assemblyBases. 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 |
|---|---|---|---|
| contigLengths | Contig lengths | list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0 | Required |
Validate nonnegative lengths and a positive safe total, sort descending and accumulate to the half-total threshold.2
N50 = contig length at cumulative sum ≥ totalAssemblyBases/2 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| n50 | N50 | integer |
| assemblyBases | Assembly bases | integer |
{
"input": {
"contigLengths": [
6,
3,
1
]
},
"output": {
"n50": 6,
"assemblyBases": 10
}
}Limitations and assumptions
N50 does not measure assembly correctness or gene completeness. Reference-based completeness uses a different threshold.
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 Assembly L50 for this operation: Count the fewest largest contigs covering half the total assembled bases. For a complementary task, use Reference NG50 for this operation: Find NG50 against half the reference genome length; flag assemblies below that threshold.
Further background: Background specification: Assembly N50.
References
-
Assembly N50 — tool.io
Similar or alternative tools
- Assembly L50
Count the fewest largest contigs covering half the total assembled bases.
- Reference NG50
Find NG50 against half the reference genome length; flag assemblies below that threshold.