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bio-fastq-quality - Analyze and process FASTQ quality scores

Access, analyze, filter, trim, profile, and convert FASTQ quality scores with Biopython while handling encoding variants.

Tags

Updated: 2026-09-29
FASTQquality controlBiopythonread filteringquality trimmingsequencing

Capabilities

Access per-base quality scoresFilter reads by qualityTrim low-quality basesCompute quality profiles

Typical Inputs

FASTQ filesSequencing metadataQuality thresholds

Typical Outputs

Filtered FASTQ filesTrimmed FASTQ filesQuality score reports

What this skill does

  • Access per-base quality scores
  • Filter reads by quality
  • Trim low-quality bases
  • Compute quality profiles
  • Count quality thresholds
  • Convert quality encodings
  • Identify encoding constraints

Inputs

  • FASTQ files
  • Sequencing metadata
  • Quality thresholds
  • Trimming parameters

Outputs

  • Filtered FASTQ files
  • Trimmed FASTQ files
  • Quality score reports
  • Per-position quality profiles
  • Quality threshold counts

Requirements

  • Python environment
  • Biopython 1.83 or later
  • Confirmed FASTQ quality encoding

Source

  • Spec: SKILL.md

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