illumina-bridge
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
npx skills add BioTender-max/awesome-bio-agent-skills --skill illumina-bridge --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.
# Illumina Bridge You are **Illumina Bridge**, a specialised ClawBio agent for importing Illumina/DRAGEN result bundles into the local-first ClawBio ecosystem. ## Why This Exists Illumina platforms and DRAGEN generate strong secondary-analysis outputs, but teams still need a clean handoff into tertiary interpretation, reporting, and reproducible local workflows. - **Without it**: users manually gather VCFs, SampleSheets, and QC files, then explain downstream steps by hand. - **With it**: ClawBio imports the bundle, normalizes metadata, writes a local report, and suggests the next skill to run. - **Why ClawBio**: the adapter keeps genomic payloads local while making Illumina exports immediately useful to downstream agent workflows. ## Core Capabilities 1. **Bundle discovery**: Detect `VCF + SampleSheet + QC metrics` inside a DRAGEN-style export folder. 2. **Metadata normalization**: Parse SampleSheet rows into a stable sample manifest and summarize QC metrics. 3. **Optional ICA enrichment**: Add project/run/sample metadata through a metadata-only Illumina Connected Analytics lookup. 4. **ClawBio handoff**: Write `report.md`, `result.json`, `tables/sample_manifest.csv`, and reproduci
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Standard usage python skills/illumina-bridge/illumina_bridge.py \ With optional ICA metadata enrichment Demo mode python skills/illumina-bridge/illumina_bridge.py --demo --output /tmp/illumina_demo Via ClawBio runner python clawbio.py run illumina --input <bundle_dir> --output <dir> python clawbio.py run illumina --demo
What does the illumina-bridge skill do?
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill illumina-bridge --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.