菜单
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.
默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。
决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
npx skills add https://github.com/PKU-EMBL/Metagenomics-Skills --skill cutadapt命令会保持在同一行。复制前请横向滚动并检查完整内容。
想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
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基于 SOC 职业分类
| 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 |
Upstream: Cutadapt
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.
Use when adapters/primers are known exactly (amplicon-like primers on shotgun libraries, custom oligos). For general Illumina shotgun QC prefer fastp.
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
| -a/-A | adapters | R1/R2 |
| -j | threads | |
fastp often enoughfastp · trimmomatic · tool-selection · metagenomics-workflow