A specialized tool for interpreting FASTQC reports to diagnose quality issues and provide actionable recommendations for NGS datasets.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install fastqc-report-interpreter
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install fastqc-report-interpreter using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is FASTQC Report Interpreter?
The FASTQC Report Interpreter is a technical asset within the Openclaw Skills library designed to streamline the quality control phase of genomic pipelines. It automates the parsing of HTML and text-based FASTQC outputs, translating complex sequencing metrics into clear, actionable insights for researchers and bioinformaticians working with RNA-seq, DNA-seq, and ChIP-seq data.
By integrating this skill into your workflow, you can move beyond simple PASS/FAIL flags to understand the underlying causes of sequencing artifacts. Whether dealing with adapter contamination, phasing effects, or PCR duplication, the FASTQC Report Interpreter provides the diagnostic logic required to ensure data integrity before proceeding to computationally expensive downstream analysis.
FASTQC Report Interpreter Use Cases
- Automating the assessment of raw sequencing data quality for large-scale NGS projects.
- Troubleshooting library preparation issues such as adapter dimers or over-amplification.
- Standardizing quality thresholds across different sequencing applications like variant calling or transcriptomics.
- Generating batch summaries for multi-sample sequencing runs to identify systematic platform errors.
How FASTQC Report Interpreter Works
- The skill ingests raw FASTQC outputs, including
.htmlreports orfastqc_data.txtfiles. - It parses key metrics such as per-base sequence quality, adapter content, and sequence duplication levels.
- Metrics are evaluated against built-in thresholds tailored for specific biological applications (e.g., DNA-seq vs. RNA-seq).
- The diagnostic engine identifies specific failures and correlates them with known sequencing issues.
- A comprehensive report is generated, offering specific remediation steps like trimming or re-running adapter removal tools.
FASTQC Report Interpreter Setup
To integrate this tool into your environment, ensure you have the necessary scripts located in your local directory. You can execute the interpreter via the command line:
# Install dependencies (ensure Python is available)
pip install -r requirements.txt
# Analyze a single FASTQC report
python scripts/fastqc_interpreter.py --input sample_fastqc.html
# Perform batch analysis on all reports in a directory
python scripts/fastqc_interpreter.py --batch "*fastqc.html" --output batch_report.pdf
FASTQC Report Interpreter Data Schema & Taxonomy
The skill organizes analysis data into structured formats for easy integration with other Openclaw Skills.
| Data Component | Format | Description |
|---|---|---|
| Input Reports | .html / .txt | Standard FASTQC output files. |
| Analysis Object | JSON/Internal | Contains quality_status, issues, and severity metrics. |
| Batch Summary | .csv / .pdf | Aggregated data for multiple samples. |
| Metrics Table | Markdown | Comparison of Q-scores, N-content, and duplication rates. |
FASTQC Report Interpreter Advanced Features
- Application-specific logic that adjusts failure thresholds based on the sequencing type (RNA-seq, DNA-seq, or ChIP-seq).
- Automated batch processing support for high-throughput sequencing facilities.
- Integrated troubleshooting guide for platform-specific errors related to Illumina, PacBio, and Oxford Nanopore.
- Custom threshold configuration via CLI arguments to match specific laboratory SOPs.
SKILL.md
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