fastq_trim

Active

declared in 1.1.0

Trim FASTQ reads: an ungapped sliding-suffix adapter match (against the same named Illumina adapters as the QC report) followed by a BWA-style 3' quality trim (the same algorithm Cutadapt's own -q option reuses), then drops reads below a minimum length. Returns the trimmed FASTQ plus before/after read-count, mean-length and mean-quality stats.

Parameters schema

{
  "type": "object",
  "required": [
    "input"
  ],
  "properties": {
    "input": {
      "type": "string",
      "description": "FASTQ text: records of an '@id' header, sequence, '+' separator and quality line (four lines each)."
    },
    "minLength": {
      "type": "integer",
      "default": 20,
      "description": "Reads shorter than this after trimming are dropped."
    },
    "qualityOffset": {
      "enum": [
        33,
        64
      ],
      "type": "integer",
      "default": 33,
      "description": "FASTQ Phred ASCII offset (33 = Sanger/Illumina 1.8+, 64 = Illumina 1.3-1.7)."
    },
    "qualityThreshold": {
      "type": "integer",
      "default": 20,
      "description": "3' quality-trim threshold (Phred score)."
    }
  },
  "additionalProperties": false
}

What this tool wraps· 0 endpoints

min confidence0.70 0.50

No endpoints wrapped at confidence ≥ 0.70.

Parent server

com.seqbench/workbench

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