---
name: bio-reporting-automated-qc-reports
source: https://app.decimal.ai/s/bio-reporting-automated-qc-reports@2/SKILL.md
source_sha256: fc022a3d0978
---

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# 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


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