Description
Trim a consecutive low-quality run from one supplied end.
Sequence text, ambiguity codes and encoded quality scores describe different information. Literal alphabets and Phred transformations can be checked without identifying a molecule or proving calibrated sequencing accuracy; missingness and reporting encodings require explicit conventions.
Trim a consecutive low-quality run from one supplied end.
When to use this tool
Use FASTQ Quality Trimming One End Budget when checking the stated sequence token, ambiguity, quality symbol or local trimming convention.
How to use the tool and how it works
- Enter scores, threshold, fromLeft. Use the units and conventions below.
- Run the tool. Correct any format, range, or cross-field input error before interpreting the output.
- Read trimmed, retained. Use the output convention below.
Trim a consecutive low-quality run from one supplied end. Require scores in [0,93] and whole threshold 0..93; remove while score < threshold, stopping at the first qualifying score, return trimmed count and retained array.1
| Input field | Meaning and units | Accepted input |
|---|---|---|
| scores | Scores | Required. Array of safe integer; maximum items 256. |
| threshold | Scores equal to threshold are retained; trimming stops at the first retained score from the selected end. | Required. Safe integer; minimum 0; maximum 93. |
| fromLeft | From Left | Required. Boolean. |
| Output field | Interpretation | Returned shape |
|---|---|---|
| trimmed | Trimmed | Required. Safe integer. |
| retained | Retained | Required. Array of safe integer; maximum items 256. |
{
"input": {
"scores": [
5,
10,
30,
4
],
"threshold": 20,
"fromLeft": true
},
"output": {
"trimmed": 2,
"retained": [
30,
4
]
}
}Limitations and assumptions
- Equality is retained and interior low scores are not revisited; this is not a sliding-window or complete FASTQ processing method.
- Inputs must satisfy both the field types and the cross-field conditions above. Invalid input causes an error; a successful false flag or documented placeholder is a different result.
- Numeric calculations use binary floating point unless exact decimal-integer arithmetic is explicitly stated. No hidden measurement tolerance or decimal rounding is added; nonfinite or out-of-contract results are rejected. Numeric signed-zero results are exported as zero.
Alternative or Complementary methods
Use a complete format-aware sequence/quality workflow and the appropriate reference/genetic code; assess biological identity and quality calibration independently.
References
Similar or alternative tools
- Bioinformatics: Fastq Quality Char Phred Score
Decode one FASTQ quality character under a supplied offset.
- Pileup Readstart Quality Symbol
Decode a pileup read-start mapping-quality symbol.