fastqc

name	fastqc
description	QC reports for Illumina FASTQ before/after trimming. Use this skill when working with fastqc: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/s-andrews/FastQC. For stage routing use tool-selection / metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["qc","fastq"]
upstream	https://github.com/s-andrews/FastQC
stage	qc

FastQC

Upstream: FastQC

Citation

Andrews, S. FastQC: a quality control tool for high throughput sequence data (2010). https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

See also docs/references.md.

Analytical thinking

FastQC is a report, not a cleaner. Use it to audit raw and cleaned reads; do trimming with fastp/cutadapt.

How to run

conda install -c bioconda fastqc  # if packaged; else follow upstream

fastqc seq/${id}_1.fq.gz seq/${id}_2.fq.gz -o temp/qc -t 8

Key parameters

| -o | output dir | HTML+zip reports | | -t | threads | |

Decision notes

• Stage: QC (report-only)
• Prefer before/after trimming for QC reports; does not modify reads
• Pair with fastp JSON/HTML for actionable filters

Related skills

fastp · kneaddata · tool-selection · metagenomics-workflow