multiqc

name	multiqc
description	MultiQC — aggregate bioinformatics QC logs into a single interactive HTML report (FastQC, fastp, Bowtie2/BWA, Samtools, QUAST, …). Use after QC/mapping steps to audit libraries before biological statistics. Upstream: https://github.com/MultiQC/MultiQC. Route via research-analysis / setup.
license	MIT
category	utilities
tags	["MultiQC","QC","report","FastQC","research-analysis"]
upstream	https://github.com/MultiQC/MultiQC
stage	qc

MultiQC

Upstream: MultiQC/MultiQC · https://multiqc.info/

Citation

Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016). https://doi.org/10.1093/bioinformatics/btw354

See also docs/references.md.

Analytical thinking

MultiQC is for technical QC dashboards, not alpha diversity or DA tests. Point it at directories of tool logs after fastqc / fastp / mapping / QUAST. Pin MultiQC version; module support varies by log format.

How to run

pip install multiqc   # or conda install -c bioconda multiqc
multiqc qc_logs/ -o multiqc_report
# optional: multiqc -c multiqc_config.yaml …

Decision tree

Need aggregated QC HTML?
├─ Yes → multiqc
├─ Biological diversity / DA → research-analysis → microeco / maaslin2
└─ Per-tool QC only → fastqc / fastp / quast skills

Related skills

research-analysis · fastqc · fastp · quast · samtools · setup · visualization · tool-selection