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openclaw-fastqc

Run FastQC on FASTQ files and report quality issues with recommended actions.

Updated Mar 30, 2026
Search Tags:#troubleshooting#quality-control#quality-metrics#fastqc#fastq#adapter-contamination#ngs-prealignment
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill openclaw-fastqc
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: openclaw-fastqc
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/openclaw-fastqc
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill openclaw-fastqc

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

FASTQ quality control is essential to identify adapter contamination, low-quality bases, and other sequencing issues before alignment.

Core Features & Use Cases

  • Run FastQC on input FASTQ files to assess quality metrics.
  • Interpret FastQC reports and highlight potential problems (adapter contamination, per-base quality drops).
  • Propose actionable next steps (trim, recheck, resequence) and generate a concise report.
  • Use case: pre-alignment QC in RNA-seq or DNA-seq pipelines to decide if data is ready for alignment.

Quick Start

Run FastQC on your input FASTQ files to generate a quality report and receive recommended next steps.

Frequently Asked Questions about openclaw-fastqc

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate FASTQ quality control and interpret adapter contamination?▼

Automated FASTQ quality control runs FastQC on input files to identify adapter contamination and per-base quality drops, then outputs a summarized report with recommended next steps for your sequencing data.

What is the best way to check if NGS data is ready for pre-alignment?▼

Pre-alignment quality control parses FastQC metrics to highlight sequencing issues like low-quality bases, providing actionable next steps such as trim, recheck, or resequence to ensure data readiness.

Do I need FastQC installed to run pre-alignment QC on RNA-seq files?▼

Yes, pre-alignment QC requires FastQC to be installed in your environment to execute quality assessments and parse metrics for RNA-seq and DNA-seq FASTQ files.

What should I do if FastQC reports adapter contamination in my FASTQ files?▼

If FastQC reports adapter contamination, the automated quality control process proposes actionable next steps like trimming adapters, rechecking metrics, or resequencing to resolve the issue.

Can I use automated FastQC reporting for DNA-seq preprocessing workflows?▼

Yes, automated FastQC reporting applies to typical DNA-seq preprocessing workflows by assessing quality metrics and recommending actions to determine if data is ready for alignment.

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