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 BioTender-max/awesome-bio-agent-skills --skill longread-sv-pipeline --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: bcftools 1.19+, minimap2 2.26+, samtools 1.19+ 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. # Long-Read SV Pipeline **"Detect structural variants from my long-read sequencing data"** → Orchestrate minimap2 alignment, SV calling (Sniffles2/cuteSV), VCF merging across callers, annotation (AnnotSV), and visualization for ONT or PacBio data. 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 k
- Version Compatibility
- 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
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 BioTender-max/awesome-bio-agent-skills --skill longread-sv-pipeline --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.