sanger-chromatogram-qa

What This Skill Does

The sanger-chromatogram-qa skill is a specialized diagnostic utility designed for the rigorous quality assessment of Sanger sequencing data. It provides a structured, reproducible environment for evaluating chromatogram files, ensuring that data analysis workflows follow consistent execution paths. By leveraging a primary script (scripts/main.py), the skill enforces explicit assumptions and clear output boundaries, allowing bioinformaticians and researchers to identify sequence quality issues, baseline noise, and signal-to-noise ratio discrepancies without ambiguity. The tool is designed to operate within a predefined scope, making it highly suitable for high-throughput or iterative data analysis where consistent reporting and documented fallbacks for missing input are mandatory requirements.

Installation

To integrate this skill into your environment, use the OpenClaw hub command-line tool. Ensure your system meets the requirement of Python 3.10+ and that all dependencies listed in the repository's requirements.txt (specifically numpy) are installed within your active environment. Execute the following command in your terminal:

clawhub install openclaw/skills/skills/aipoch-ai/sanger-chromatogram-qa

Once installed, verify the installation by navigating to the skill directory and running python -m py_compile scripts/main.py. If this returns no errors, the environment is correctly configured.

Use Cases

This skill is ideal for projects where manual chromatogram review is unfeasible due to volume or where auditing is required for regulatory compliance. Use it to automate the verification of trace file quality before downstream analysis like alignment or assembly. It is also perfect for screening datasets for specific degradation signatures or threshold-based failures. When a file fails to meet quality thresholds, the skill provides a clear, documented path for error handling, preventing corrupt or low-quality data from proceeding further in your pipeline.

Example Prompts

1. "Run the sanger-chromatogram-qa on all files in the ./sequencing-data directory, setting the phred score threshold to 20, and output the summary to ./results/qc_report.json."
2. "Perform a quality assessment for file sample_A_01.ab1. If the script encounters missing input or low trace signals, generate a fallback report detailing the specific failure mode."
3. "Evaluate the batch of chromatograms in the current directory. Please ensure the output strictly follows the structured format defined in the documentation and include any assumptions made regarding noise filtering."

Tips & Limitations

The skill is strictly bounded by the parameters defined in scripts/main.py. Users should familiarize themselves with the CONFIG block within the script before processing large datasets to ensure that thresholds match their specific experimental needs. It is not intended for de novo base calling, but rather for quality assessment of existing trace files. Always confirm the file paths and ensure the input directory is isolated to prevent accidental processing of irrelevant files. Because the tool relies on numpy, ensure your environment's numerical libraries are updated to prevent rounding errors or processing bottlenecks during high-volume analysis.