bio-workflows-longread-sv-pipeline
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.
npx skills add majiayu000/claude-skill-registry --skill longread-sv-pipeline-gptomics-bioskills --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.
# Long-Read SV Pipeline Complete workflow for detecting structural variants from ONT or PacBio long-read data. ## Workflow Overview ``` Long reads (ONT/PacBio) | v [1. QC] ----------------> NanoPlot | v [2. Alignment] ---------> minimap2 | v [3. SV Calling] --------> Sniffles / cuteSV | v [4. Filtering] ---------> bcftools | v [5. Annotation] --------> AnnotSV (optional) | v Filtered SV VCF ``` ## Primary Path: minimap2 + Sniffles ### Step 1: Quality Control ```bash # ONT reads QC NanoPlot --fastq reads.fastq.gz \ --outdir nanoplot_output \ --threads 8 # Check key metrics # - Read N50 should be >10kb # - Mean quality >Q10 # - Total bases sufficient for coverage ``` ### Step 2: Alignment with minimap2 ```bash # ONT reads minimap2 -ax map-ont \ -t 16 \ --MD \ -Y \ reference.fa \ reads.fastq.gz | \ samtools sort -@ 4 -o aligned.bam samtools index aligned.bam # PacBio HiFi minimap2 -ax map-hifi \ -t 16 \ --MD \ -Y \ reference.fa \ reads.fastq.gz | \ samtools sort -@ 4 -o aligned.bam # PacBio CLR minimap2 -ax map-pb \ -t 16 \ --MD \ -Y \ reference.fa \ reads.fastq.gz | \ samtools sort -@ 4 -o aligned.bam ``` **QC Checkpoint:** Check alignment stats ```bash samtools flagstat aligned.bam
- Workflow Overview
- Primary Path: minimap2 + Sniffles
- Step 1: Quality Control
- Step 2: Alignment with minimap2
- Step 3: SV Calling with Sniffles
- Alternative: cuteSV
- Step 4: Filtering
- Step 5: Annotation (Optional)
- Multi-Sample SV Calling
- Parameter Recommendations
- SV Types Detected
- Troubleshooting
- Complete Pipeline Script
- Related Skills
ONT reads QC NanoPlot --fastq reads.fastq.gz \ Check key metrics ONT reads minimap2 -ax map-ont \ reference.fa \ reads.fastq.gz | \ samtools sort -@ 4 -o aligned.bam samtools index aligned.bam PacBio HiFi
What does the bio-workflows-longread-sv-pipeline skill do?
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill longread-sv-pipeline-gptomics-bioskills --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 majiayu000/claude-skill-registry, a repository with 534 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.