| 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
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
