bio-read-qc-quality-filtering
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-quality-filtering --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Trimmomatic 0.39+, cutadapt 4.4+, fastp 0.23+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Quality Filtering 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 Quality Operations ### Single-End Mode ```bash trimmomatic SE -phred33 \ input.fastq.gz output.fastq.gz \ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ``` ### Paired-End Mode ```bash trimmomatic PE -phred33 -threads 4 \ input_R1.fastq.gz input_R2.fastq.gz \ output_R1_paired.fastq.gz output_R1_unpaired.fastq.gz \ output_R2_paired.fastq.gz output_R2_unpaired.fastq.gz \ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:
- Version Compatibility
- Trimmomatic Quality Operations
- Single-End Mode
- Paired-End Mode
- Trimmomatic Operations
- Common Trimmomatic Recipes
- SLIDINGWINDOW Details
- fastp Quality Filtering
- Basic Quality Filtering
- fastp Quality Options
- Paired-End with fastp
- Length Filtering
- Cutadapt Quality Trimming
- Combined Adapter + Quality Trimming
trimmomatic SE -phred33 \ input.fastq.gz output.fastq.gz \ trimmomatic PE -phred33 -threads 4 \ input_R1.fastq.gz input_R2.fastq.gz \ output_R1_paired.fastq.gz output_R1_unpaired.fastq.gz \ output_R2_paired.fastq.gz output_R2_unpaired.fastq.gz \ Standard quality trimming trimmomatic SE input.fq output.fq \ Aggressive 3' trimming Trim both ends, strict filtering
What does the bio-read-qc-quality-filtering skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-read-qc-quality-filtering --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.