Reference NG50

Find NG50 against half the reference genome length; flag assemblies below that threshold.

Description

NG50 uses half a reference genome as its cumulative length target.

NG50 uses half a reference genome as its cumulative length target. Unlike N50, an incomplete assembly may never reach that reference-based threshold.^[1]

Find NG50 against half the reference genome length; flag assemblies below that threshold.

When to use Reference NG50

Use this for the following task: Find NG50 against half the reference genome length; flag assemblies below that threshold.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Reference NG50 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, referenceGenomeBases using the field table, then run the tool.
Read ng50, thresholdReached. 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
referenceGenomeBases	Reference genome length in bases; half this length sets the NG50 threshold.	integer; minimum 1	Required

Require a positive reference length and supported contig lengths. Sort lengths descending, accumulate and report whether the reference threshold was reached.^[2]

NG50 = length at first descending cumulative sum ≥ referenceGenomeBases/2

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
ng50	NG50	integer
thresholdReached	Threshold reached	boolean

json

{
  "input": {
    "contigLengths": [
      6,
      3,
      1
    ],
    "referenceGenomeBases": 20
  },
  "output": {
    "ng50": 1,
    "thresholdReached": true
  }
}

Limitations and assumptions

If the threshold is not reached, ng50 is 0 and thresholdReached is false. Contiguity does not measure assembly correctness.

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 Assembly L50 for this operation: Count the fewest largest contigs covering half the total assembled bases.

Further background: Background specification: Reference NG50.

References

Background specification: Reference NG50 — QUAST
Reference NG50 — tool.io

Similar or alternative tools

Assembly N50
Find the contig length at which descending cumulative length reaches half the assembly.
Assembly L50
Count the fewest largest contigs covering half the total assembled bases.