Runs FastQC and MultiQC pipelines on FASTQ files and generates QC visualizations.
npx skills add https://github.com/ClawBio/ClawBio --skill bioqc-mcp
Please help me install this Agent Skill. Skill: bioqc-mcp Source: https://github.com/ClawBio/ClawBio/tree/main/skills/bioqc-mcp Command: npx skills add https://github.com/ClawBio/ClawBio --skill bioqc-mcp
Running sequencing quality control requires manually chaining FastQC, MultiQC, log parsing, and custom plotting scripts. This Skill automates the entire workflow: it discovers FASTQ files, executes FastQC in parallel, aggregates results with MultiQC, extracts per-base quality and GC content metrics, and renders publication-quality charts, all locally.
Ask the agent to run quality control on your FASTQ directory, or execute the demo with python clawbio.py run bioqc --demo to generate a synthetic QC report with figures.
High-intent search queries and answers about installing and using this skill.
Point the skill at a directory containing FASTQ files and it discovers all .fastq, .fq, .fastq.gz, and .fq.gz files, runs FastQC in parallel with configurable threads, then aggregates results with MultiQC into a single interactive HTML report.
The skill parses fastqc_data.txt to extract per-base sequence quality and per-sequence GC content blocks, then renders line charts, violin plots, heatmaps, and 20+ other chart types using Matplotlib and Seaborn, saved as PNG files.
Yes, the skill runs as an MCP stdio server exposing 10 tools including run_fastqc, run_multiqc, list_fastq_files, and generate_chart. Start it with the --mode mcp flag and register it in your MCP client configuration.
The pipeline requires fastqc and multiqc binaries on your system PATH. Install FastQC via your package manager (e.g., brew install fastqc) and MultiQC via pip install multiqc, then rerun the pipeline.
No, all FastQC and MultiQC processing runs strictly locally via subprocess calls with no shell interpolation. No genetic data is uploaded anywhere, and every report includes a research-use disclaimer.
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mims-harvardRun FastQC quality control on FASTQ reads and decide adapter or quality trimming with fastp.
MubasherMohammedAggregate bioinformatics QC reports into MultiQC HTML and ClawBio markdown summaries.
