skills.rest
jaechang-hits
jaechang-hitsCOMMUNITY
Explore all skills by this author →
GitHub

multiqc-qc-reports

Aggregate QC outputs from over 150 bioinformatics tools into interactive HTML reports.

298|27|Updated Feb 18, 2026
Search Tags:#report generation#bioinformatics#data aggregation#multiqc#ngs#qc reports
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill multiqc-qc-reports
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: multiqc-qc-reports
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/multiqc-qc-reports
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill multiqc-qc-reports

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill automates the aggregation of quality control (QC) reports from over 150 bioinformatics tools, consolidating them into a single, interactive HTML report for efficient review of next-generation sequencing (NGS) pipeline outputs.

Core Features & Use Cases

  • Multi-Sample Aggregation: Parses QC logs from tools like FastQC, samtools, STAR, Salmon, and GATK across numerous samples.
  • Interactive HTML Reports: Generates comprehensive reports with plots, tables, and configurable thresholds.
  • Use Case: After running a full RNA-seq pipeline on 48 samples, use this Skill to generate a single report summarizing the QC metrics for all samples, highlighting any potential issues or batch effects.

Quick Start

Run MultiQC on the current directory to generate a consolidated QC report.

Frequently Asked Questions about multiqc-qc-reports

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

FAQPage Schema
How do I aggregate bioinformatics QC reports from multiple samples into one file?▼

Aggregating bioinformatics QC reports involves scanning directories for logs from tools like FastQC, samtools, STAR, and GATK, then merging statistics across samples into a single interactive HTML report.

What is the best way to generate a multi-sample QC report for an RNA-seq pipeline?▼

Generating a multi-sample QC report for an RNA-seq pipeline is best done by parsing logs from tools like Salmon and STAR across all samples, highlighting potential issues or batch effects in a single interactive report.

Does MultiQC support quality control outputs from GATK and samtools?▼

MultiQC supports quality control outputs from GATK and samtools, along with over 150 other bioinformatics tools, parsing their logs to merge statistics across samples with interactive plots.

Can I configure thresholds for QC metrics in an NGS pipeline report?▼

Configuring thresholds for QC metrics in an NGS pipeline report is possible, allowing you to generate comprehensive reports with plots, tables, and configurable thresholds to highlight potential issues.

Why do I need to aggregate FastQC results across numerous samples?▼

Aggregating FastQC results across numerous samples is needed to review multi-sample NGS pipeline outputs efficiently, consolidating individual logs into a single interactive HTML report to spot batch effects.

Related Skills

Explore More Data & Analytics Skills→
MubasherMohammedMubasherMohammed

multiqc-reporter

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

Community
Intermediate
pradyumnasagarpradyumnasagar
6

pysam-genomics

Read, modify, filter, and write BAM/CRAM/VCF files via pysam.

Community
Intermediate
ovachieverovachiever
52

deeptools

Convert BAM alignments into normalized coverage tracks and generate QC metrics.

Community
Advanced
MDheweiMDhewei
64

crispr-screen-qc

Analyze sgRNA read counts to detect quality issues in pooled CRISPR screens.

Community
Advanced