BUSCO Completeness
Calculate complete and single-copy completeness from exclusive BUSCO-style category counts.
Description
BUSCO-style summaries partition expected orthologs into complete single-copy, complete duplicated, fragmented and missing categories.
BUSCO-style summaries partition expected orthologs into complete single-copy, complete duplicated, fragmented and missing categories. Complete duplicated genes still contribute to complete percentage.1
Calculate complete and single-copy completeness from exclusive BUSCO-style category counts.
When to use BUSCO Completeness
Use this for the following task: Calculate complete and single-copy completeness from exclusive BUSCO-style category counts.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use BUSCO Completeness 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 singleCopyComplete, duplicatedComplete, fragmented, missing using the field table, then run the tool.
- Read completePercent, singleCopyPercent, totalOrthologs. 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 |
|---|---|---|---|
| singleCopyComplete | Single copy complete | integer; minimum 0 | Required |
| duplicatedComplete | Duplicated complete | integer; minimum 0 | Required |
| fragmented | Fragmented | integer; minimum 0 | Required |
| missing | Missing | integer; minimum 0 | Required |
Use exclusive nonnegative category counts with a positive safe total. Add categories and return the two completeness percentages.2
complete% = 100(singleCopy+duplicated)/total; singleCopy% = 100 singleCopy/total This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| completePercent | Complete percent | number |
| singleCopyPercent | Single copy percent | number |
| totalOrthologs | Total orthologs | integer |
{
"input": {
"singleCopyComplete": 80,
"duplicatedComplete": 10,
"fragmented": 5,
"missing": 5
},
"output": {
"completePercent": 90,
"singleCopyPercent": 80,
"totalOrthologs": 100
}
}Limitations and assumptions
No BUSCO search is run. Counts and lineage appropriateness must be established upstream; category overlap would corrupt the denominator.
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: BUSCO Completeness.
References
-
BUSCO Completeness — 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.