Files & formats

FASTQ Adapter & Quality Trimmer

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.

post/fastq_trim

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/fastq_trim
  • Auth: none required

Request body

inputstring required

FASTQ text: records of an '@id' header, sequence, '+' separator and quality line (four lines each).

qualityOffset33 | 64

ASCII offset of the FASTQ quality string. 33 for anything modern, 64 for pre-1.8 Illumina.

qualityThresholdinteger

3' quality-trim threshold (Phred score).

minLengthinteger

Reads shorter than this after trimming are dropped.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.