---
name: bio-reporting-automated-qc-reports
description: Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
tool_type: cli
primary_tool: multiqc
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
  - read_file
  - run_shell_command
---

<!--
# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

-->


# Automated QC Reports with MultiQC

## Basic Usage

```bash
# Aggregate all QC outputs in directory
multiqc results/ -o qc_report/

# Specify output name
multiqc results/ -n my_project_qc

# Include specific tools only
multiqc results/ --module fastqc --module star
```

## Supported Tools

MultiQC recognizes outputs from 100+ bioinformatics tools:

| Category | Tools |
|----------|-------|
| Read QC | FastQC, fastp, Cutadapt |
| Alignment | STAR, HISAT2, BWA, Bowtie2 |
| Quantification | featureCounts, Salmon, kallisto |
| Variant Calling | bcftools, GATK |
| Single-cell | CellRanger, STARsolo |

## Configuration

Create `multiqc_config.yaml`:

```yaml
title: "RNA-seq QC Report"
subtitle: "Project XYZ"
intro_text: "QC metrics for all samples"

# Custom sample name cleaning
extra_fn_clean_exts:
  - '.sorted'
  - '.dedup'

# Report sections to include
module_order:
  - fastqc
  - star
  - featurecounts

# Highlight samples
table_cond_formatting_rules:
  pct_mapped:
    fail: [{lt: 50}]
    warn: [{lt: 70}]
```

## Custom Data

```bash
# Add custom data file
# File format: sample\tmetric1\tmetric2
multiqc results/ --data-format tsv --custom-data-file custom_metrics.tsv
```

## Python API

```python
from multiqc import run as multiqc_run

# Run programmatically
multiqc_run(analysis_dir='results/', outdir='qc_report/')
```

## Related Skills

- read-qc/quality-reports - Generate input FastQC reports
- read-qc/fastp-workflow - Preprocessing QC
- workflows/rnaseq-to-de - Full workflow with QC


<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

---
Source attribution: GPTomics
Original project: https://github.com/GPTomics/bioSkills
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Dave AI.

## Upstream license notice

MIT License

Copyright (c) 2026 FridrichMethod

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

---

NOTE ON BUNDLED CONTENT

This repository aggregates skills from multiple upstream projects (see the
README for the source list). Each `skills/<name>/` directory may carry its
own license inherited from its upstream source. The MIT license above
applies to this repository's curation and the scripts/workflows in `/`,
`/scripts/`, and `/.github/` — not to the upstream skill content itself.
Consult the upstream repository linked in the README and any LICENSE
file inside a skill directory before reusing skill content commercially.



# Dave AI resource metadata

Creator / publisher: GPTomics
Original project: https://github.com/GPTomics/bioSkills
Attribution basis: Exact package in biomedical source index and publisher source table

Fields of work: Data & Analytics, Education & Research
Roles: Business Intelligence Analyst, Data Analyst, Researcher
Specialties: API, Backend, Frontend
Tools: Multiqc
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 165bb258fc0873c969d9fb46b8805790395f6cbc267d488c0a8a6d1317e04765
Metadata reviewed: 2026-10-27
This metadata supersedes earlier Dave AI catalog attribution. Original instruction and supporting files are preserved.