multiqc

name	multiqc
description	Use when you need to aggregate quality control reports from multiple bioinformatics tools into a single HTML report
disable-model-invocation	true
user-invocable	true

multiqc

Quick Start

• Command: multiqc [OPTIONS] [ANALYSIS DIRECTORY]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/multiqc
• Version: 1.33
• Full reference: See references/help.md for complete options and usage

When To Use This Tool

• Aggregate many per-sample QC or analysis reports into one HTML dashboard.
• Summarize outputs from FastQC, cutadapt, aligners, quantifiers, and many other tools.
• Use it after per-sample processing is done, not as a first-pass QC tool.
• Best for cohort-level review and sample-to-sample comparison.

Common Patterns

# 1) Scan the current analysis directory
multiqc .

# 2) Write report into a dedicated output directory
multiqc results -o multiqc_out -n project_multiqc.html

# 3) Limit or exclude modules
multiqc results -m fastqc -m cutadapt -e star

# 4) Prefix sample names with directory names to reduce collisions
multiqc results -d

Recommended Workflow

1. Run per-sample QC and analysis tools first.
2. Point MultiQC at the project results tree or a curated file list.
3. Review sample naming, module detection, and missing-module warnings before trusting the report.
4. Archive the HTML plus parsed data directory if the summary will be cited or shared.

Guardrails

• MultiQC only summarizes logs it recognizes; if upstream tools did not emit report files, there is nothing to aggregate.
• Re-running in the same output location often needs -f/--force.
• Sample name collisions can silently confuse interpretation; use -d, -s, or renaming options when needed.
• If the report looks suspiciously sparse, check whether modules were excluded or whether files were ignored by glob patterns.