Personal-Genome-Pipeline

Step 28: MultiQC Aggregated QC Report

Scans the sample directory for QC outputs from all pipeline steps and combines them into a single interactive HTML dashboard.

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What It Does

MultiQC auto-discovers output files from supported bioinformatics tools and renders them into a unified report with:

• Summary statistics table — key metrics from each tool in one view
• Interactive plots — quality distributions, coverage curves, adapter content
• Before/after comparisons — fastp filtering impact

Why

Without MultiQC, you need to open separate reports from each tool (fastp HTML, mosdepth summary, samtools flagstat). MultiQC combines everything into one page, making it easy to spot problems at a glance.

Tool

MultiQC v1.33 — aggregate bioinformatics QC reports.

• Paper: Ewels et al., Bioinformatics 2016 (doi:10.1093/bioinformatics/btw354)
• Source: github.com/MultiQC/MultiQC

Docker Image

quay.io/biocontainers/multiqc:1.33--pyhdfd78af_0

Command

export GENOME_DIR=/path/to/data
./scripts/28-multiqc.sh <sample_name>

Discovered Tools

MultiQC scans the entire sample directory and auto-detects outputs from these pipeline tools:

Tool	File Pattern	Pipeline Step
fastp	*_fastp.json	Step 1b (QC + trimming)
samtools flagstat	*_flagstat.txt	Generated automatically
mosdepth	*.mosdepth.summary.txt, *.mosdepth.global.dist.txt	Step 16b

The script generates samtools flagstat output automatically if a BAM exists but no flagstat file is present.

Output

File	Location	Description
HTML report	multiqc/multiqc_report.html	Interactive QC dashboard (open in browser)

Runtime

< 1 minute. MultiQC only parses summary files, not raw data.

Notes

• MultiQC runs after all other steps to capture the most outputs. In run-all.sh, it runs alongside the HTML summary report at the end
• The report title includes the sample name for easy identification
• If you add new tools to the pipeline that MultiQC supports, their outputs are picked up automatically on the next run
• To re-generate the report (e.g., after running additional steps), delete the multiqc/ directory and re-run

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