Assembly L50
Count the fewest largest contigs covering half the total assembled bases.
Description
Assembly L50 counts how many of the largest contigs cover half the assembled bases.
Assembly L50 counts how many of the largest contigs cover half the assembled bases. It complements N50, which reports the boundary contig’s length.1
Count the fewest largest contigs covering half the total assembled bases.
When to use Assembly L50
Use this for the following task: Count the fewest largest contigs covering half the total assembled bases.
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 L50 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 l50, 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 lengths and a positive safe total, sort descending, and count contigs through the half-assembly crossing.2
L50 = smallest descending prefix count with bases ≥ total/2 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| l50 | L50 | integer |
| assemblyBases | Assembly bases | integer |
{
"input": {
"contigLengths": [
6,
3,
1
]
},
"output": {
"l50": 1,
"assemblyBases": 10
}
}Limitations and assumptions
This is a contiguity metric, not a measure of sequence accuracy. Assembly size affects its interpretation.
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 N50 for this operation: Find the contig length at which descending cumulative length reaches half the assembly. 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 L50.
References
-
Assembly L50 — tool.io
Similar or alternative tools
- Assembly N50
Find the contig length at which descending cumulative length reaches half the assembly.
- Reference NG50
Find NG50 against half the reference genome length; flag assemblies below that threshold.