cutadapt

name	cutadapt
description	Adapter/primer trimming for short and long reads. Use this skill when working with cutadapt: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/marcelm/cutadapt. For stage routing use tool-selection / metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["qc","adapters"]
upstream	https://github.com/marcelm/cutadapt
stage	qc

Cutadapt

Upstream: Cutadapt

Citation

Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011). https://doi.org/10.14806/ej.17.1.200

See also docs/references.md.

Analytical thinking

Use when adapters/primers are known exactly (amplicon-like primers on shotgun libraries, custom oligos). For general Illumina shotgun QC prefer fastp.

How to run

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

cutadapt -j 8 -a AGATCGGAAGAGC -A AGATCGGAAGAGC \
  -o temp/qc/${id}_1.fq.gz -p temp/qc/${id}_2.fq.gz \
  seq/${id}_1.fq.gz seq/${id}_2.fq.gz

Key parameters

| -a/-A | adapters | R1/R2 | | -j | threads | |

Decision notes

• Stage: QC — adapter/primer trimming before host depletion / assembly
• Prefer when custom adapters or amplicon primers matter; else fastp often enough
• Keep trimmed PE pairing consistent for KneadData / assembly

Related skills

fastp · trimmomatic · tool-selection · metagenomics-workflow