multiqc-reporter

Aggregate bioinformatics QC reports into MultiQC HTML and ClawBio markdown summaries.

Updated May 10, 2026

Search Tags:#quality control #bioinformatics #genomics #MultiQC #QC reporting

Ready to run

npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill multiqc-reporter

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: multiqc-reporter
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/multiqc-reporter
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill multiqc-reporter

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires multiqc, clawbio, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Aggregates quality control (QC) reports from various bioinformatics tools into a single, comprehensive report, saving users time and effort.

Core Features & Use Cases

Aggregates QC reports: Combines outputs from tools like FastQC, fastp, STAR, and Picard into a single MultiQC HTML report.
Markdown summary: Provides a ClawBio markdown summary with per-sample QC metrics for easy analysis.
Use Case: If you have run multiple QC tools on your sequencing data, this skill can create a consolidated report that summarizes the results across all tools.

Quick Start

Run MultiQC on your sample directories to generate a report.

Frequently Asked Questions about multiqc-reporter

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

FAQPage Schema

How do I aggregate bioinformatics QC reports from multiple tools into a single report?▼

You can aggregate bioinformatics QC reports from tools like FastQC, fastp, STAR, and Picard into a single consolidated MultiQC HTML report and a ClawBio markdown summary containing per-sample metrics.

What is the best way to combine FastQC and Picard quality control results for genomics workflows?▼

The best way to combine FastQC and Picard results is to use MultiQC to parse the output directories, generating a single consolidated HTML report that summarizes quality control metrics across all samples and tools.

Does MultiQC work with STAR and fastp outputs for genomics quality control?▼

Yes, MultiQC works with STAR and fastp outputs by parsing their log files and summary statistics, allowing you to aggregate genomics quality control data into one comprehensive HTML report.

Can I generate a markdown summary of per-sample QC metrics alongside the MultiQC HTML report?▼

Yes, you can generate a ClawBio markdown summary alongside the MultiQC HTML report, providing per-sample quality control metrics in a text format that is easy to analyze and share.

Do I need Python and the ClawBio package to aggregate QC reports?▼

Yes, you need Python with the multiqc and ClawBio packages installed to aggregate quality control reports, as the workflow relies on these dependencies to parse inputs and generate the consolidated HTML and markdown outputs.

How do I run MultiQC on multiple sample directories to create a consolidated QC report?▼

You run MultiQC on your sample directories by pointing it to the folders containing outputs from tools like FastQC and STAR, which then parses the logs and generates a single aggregated HTML quality control report.