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bio-read-qc-quality-filtering
Maintainer FreedomIntelligence · Last updated April 1, 2026
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have poor quality tails or require minimum quality for downstream analysis.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-read-qc-quality-filtering
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: trimmomatic PE with SLIDINGWINDOW and MINLEN options.
- CLI: fastp --qualified_quality_phred 20 --length_required 50.
- Trim low-quality bases and filter reads using Trimmomatic sliding window or fastp quality filtering.
- Filter reads by quality" → Remove low-quality bases and discard reads below quality/length thresholds. CLI: trimmomatic PE with SLIDINGWINDOW and MINLEN options CLI: fastp --qualified_quality_phred 20 --length_required 50.
- trimmomatic SE input.fq output.fq \ SLIDINGWINDOW:4:20 MINLEN:36.
Source Doc
Excerpt From SKILL.md
Trimmomatic Operations
| Operation | Syntax | Description |
|---|---|---|
| LEADING | LEADING:Q | Remove leading bases below quality Q |
| TRAILING | TRAILING:Q | Remove trailing bases below quality Q |
| SLIDINGWINDOW | SLIDINGWINDOW:W:Q | Cut when W-bp window average < Q |
| MINLEN | MINLEN:L | Discard reads shorter than L |
| CROP | CROP:L | Cut read to max length L |
| HEADCROP | HEADCROP:N | Remove first N bases |
| AVGQUAL | AVGQUAL:Q | Drop read if average quality < Q |
| MAXINFO | MAXINFO:L:S | Balance length and quality |
| TOPHRED33 | TOPHRED33 | Convert to Phred33 encoding |
| TOPHRED64 | TOPHRED64 | Convert to Phred64 encoding |
Aggressive 3' trimming
trimmomatic SE input.fq output.fq
TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:36
Trim both ends, strict filtering
trimmomatic SE input.fq output.fq
LEADING:10 TRAILING:10 SLIDINGWINDOW:4:25 MINLEN:50
Use cases
- Use when reads have poor quality tails or require minimum quality for downstream analysis.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- adapter-trimming - Remove adapters before quality filtering
- quality-reports - Check quality before/after filtering
- fastp-workflow - All-in-one preprocessing
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