| name | trimmomatic |
| description | Flexible Illumina adapter/quality trimmer. Use this skill when working with trimmomatic: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/usadellab/Trimmomatic. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["qc","trimming"] |
| upstream | https://github.com/usadellab/Trimmomatic |
| stage | qc |
Trimmomatic
Upstream: Trimmomatic
Citation
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014). https://doi.org/10.1093/bioinformatics/btu170
See also docs/references.md.
Analytical thinking
Prefer fastp for most shotgun runs (speed + JSON). Use Trimmomatic when a lab SOP already pins ILLUMINACLIP settings.
How to run
conda install -c bioconda trimmomatic
trimmomatic PE -threads 8 \
seq/${id}_1.fq.gz seq/${id}_2.fq.gz \
temp/qc/${id}_1P.fq.gz temp/qc/${id}_1U.fq.gz \
temp/qc/${id}_2P.fq.gz temp/qc/${id}_2U.fq.gz \
ILLUMINACLIP:adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:50
Key parameters
| ILLUMINACLIP | adapter fasta | Required |
| SLIDINGWINDOW | 4:20 typical | |
| MINLEN | ≥50 | |
Decision notes
- Stage: QC (legacy Illumina trimmer)
- Prefer
fastp for new pipelines unless reproducing Trimmomatic Methods
- Keep PE pairing; archive trim logs
Related skills
fastp · fastqc · kneaddata · tool-selection · metagenomics-workflow
