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bio-read-qc-adapter-trimming
Maintainer FreedomIntelligence · Last updated April 1, 2026
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-adapter-trimming
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: cutadapt -a ADAPTER -o out.fq in.fq or trimmomatic PE with ILLUMINACLIP.
- CLI: fastp -i in.fq -o out.fq (auto-detects adapters).
- Remove sequencing adapters from reads using Cutadapt (precise, flexible) or Trimmomatic (paired-end optimized).
- Trim adapters from reads" → Remove sequencing adapter sequences from FASTQ reads to prevent adapter contamination in downstream alignment. CLI: cutadapt -a ADAPTER -o out.fq in.fq or trimmomatic PE with ILLUMINACLIP CLI: fastp -i in.fq -o out.fq (auto-detects adapters).
- cutadapt -a AGATCGGAAGAGC -o trimmed.fastq.gz sample.fastq.gz.
Source Doc
Excerpt From SKILL.md
Common Adapter Sequences
| Platform/Kit | Adapter | Sequence |
|---|---|---|
| Illumina TruSeq | Read 1 3' | AGATCGGAAGAGCACACGTCTGAACTCCAGTCA |
| Illumina TruSeq | Read 2 3' | AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT |
| Nextera | Transposase | CTGTCTCTTATACACATCT |
| Small RNA | 3' adapter | TGGAATTCTCGGGTGCCAAGG |
| Poly-A | Poly-A tail | AAAAAAAAAAAAAAAA |
5' adapter
cutadapt -g ACGTACGT -o trimmed.fastq.gz sample.fastq.gz
Both ends
cutadapt -a ADAPTER1 -g ADAPTER2 -o trimmed.fastq.gz sample.fastq.gz
Use cases
- Use when FastQC shows adapter contamination or before alignment of short reads.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- quality-reports - Check adapter content with FastQC
- quality-filtering - Quality trimming after adapter removal
- fastp-workflow - Combined adapter and quality trimming
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