| name | fastp |
| description | Ultra-fast FASTQ QC/adapter trimming for Illumina/MGI short reads. Use this skill when working with fastp: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/OpenGene/fastp. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["qc","fastq","trimming"] |
| upstream | https://github.com/OpenGene/fastp |
fastp
Upstream: OpenGene/fastp
Citation
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018). https://doi.org/10.1093/bioinformatics/bty560
See also docs/references.md.
Analytical thinking
Use fastp before host depletion or assembly so adapter/low-quality bases do
not create false k-mers or broken PE pairs. Prefer fastp for short reads; for
ONT/PacBio use long-read QC tools (e.g. fastplong), not fastp.
Always archive HTML/JSON reports — they are the audit trail for “reads were clean”.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Input | Illumina/MGI PE or SE FASTQ(.gz) | Phred33 |
| CPU | 4 threads | 8–16 |
| Disk | ~1–2× input for outputs | Separate temp/qc |
How to run
conda install -c bioconda fastp
fastp \
-i seq/${id}_1.fq.gz -I seq/${id}_2.fq.gz \
-o temp/qc/${id}_1.fastq -O temp/qc/${id}_2.fastq \
-j temp/qc/${id}_fastp.json -h temp/qc/${id}_fastp.html \
-w 8
Key parameters
| Parameter | Typical | Notes |
|---|
-i/-I | R1/R2 | Required for PE |
-o/-O | cleaned FASTQ | Keep uncompressed only if KneadData expects it |
-j/-h | JSON/HTML | Always keep |
-w | 8 | Threads |
--detect_adapter_for_pe | on when unsure | Auto adapter detection |
Output
temp/qc/${id}_1.fastq
temp/qc/${id}_2.fastq
temp/qc/${id}_fastp.json
temp/qc/${id}_fastp.html
Decision tree
Short-read shotgun?
├─ Yes → fastp
└─ Long-read only → not fastp (use long-read QC)
Verify
seqkit stat temp/qc/${id}_*.fastq
grep -E 'total reads|adapter' temp/qc/${id}_fastp.json | head
Related skills
kneaddata → next for host removal · setup for env install
