Duplicated Fragmentation Warning Completeness Caveat Flag Checker
Flag supplied complete-duplicated and fragmented ortholog evidence; not a BUSCO run or proof of contamination/assembly failure.
Description
Flag supplied complete-duplicated and fragmented ortholog evidence; not a BUSCO run or proof of contamination/assembly failure.
Assembly-completeness summaries can hide duplicated or fragmented ortholog categories. Separate flags preserve those caveats without reducing assembly quality to one percentage.
When to use this tool
Flag supplied complete-duplicated and fragmented ortholog evidence; not a BUSCO run or proof of contamination/assembly failure.
- Prepare the supplied duplicatedComplete, fragmented, totalOrthologs 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 duplicatedComplete, fragmented, totalOrthologs. 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.duplicationCaveat, result.fragmentationCaveat, result.completenessAloneEstablishesAssemblyQuality. Interpret false, null and empty lists using the distinctions below; they can be valid outputs.
Validate duplicatedComplete and fragmented as nonnegative disjoint counts within positive totalOrthologs. Set their caveat flags when each count exceeds zero, and return completenessAloneEstablishesAssemblyQuality false.1
| Input field | Meaning and representation | Accepted input |
|---|---|---|
| duplicatedComplete | duplicated complete. | Finite number |
| fragmented | fragmented. | Finite number |
| totalOrthologs | total orthologs. | Finite number |
| Output field | Interpretation |
|---|---|
| result | Object containing the named outputs below. |
| result.duplicationCaveat | Flag for duplication caveat under the exact condition described above. |
| result.fragmentationCaveat | Flag for fragmentation caveat under the exact condition described above. |
| result.completenessAloneEstablishesAssemblyQuality | Flag for completeness alone establishes assembly quality under the exact condition described above. |
{
"input": {
"duplicatedComplete": 1,
"fragmented": 2,
"totalOrthologs": 10
},
"output": {
"result": {
"duplicationCaveat": true,
"fragmentationCaveat": true,
"completenessAloneEstablishesAssemblyQuality": false
}
}
}Limitations and assumptions
- The tool does not run an ortholog search or calculate full completeness categories. Duplication and fragmentation can have several causes; the flags do not diagnose contamination or assembly error.
- 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
- busco completeness
BUSCO-style summaries partition expected orthologs into complete single-copy, complete duplicated, fragmented and missing categories.
- CADD-like Combined Deleteriousness Score Threshold Gate Checker
Screen a caller-supplied CADD-like score and threshold; does not calculate CADD or infer pathogenicity.