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MubasherMohammed
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illumina-bridge

Import DRAGEN result bundles with VCFs, SampleSheets, and QC metrics into ClawBio.

Updated May 10, 2026
Search Tags:#bioinformatics#genomics#ica#illumina#dragen
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill illumina-bridge
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: illumina-bridge
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/illumina-bridge
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill illumina-bridge

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the import of Illumina result bundles into the local-first ClawBio ecosystem, streamlining tertiary analysis and downstream routing.

Core Features & Use Cases

  • Bundle Import: Automatically discovers and imports DRAGEN-exported Illumina result bundles.
  • Metadata Normalization: Parses SampleSheet and QC metrics into a stable format.
  • ICA Enrichment: Optionally enriches metadata using Illumina Connected Analytics.
  • ClawBio Handoff: Writes reports, manifests, and suggests downstream analysis steps.
  • Use Case: After running a DRAGEN analysis, use this Skill to import the results into ClawBio for further analysis and reporting.

Quick Start

Run the 'illumina-bridge' skill with the input bundle directory and output directory:

python skills/illumina-bridge/illumina_bridge.py --input <bundle_dir> --output <report_dir>

Frequently Asked Questions about illumina-bridge

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I import Illumina DRAGEN result bundles for tertiary analysis?▼

To import Illumina DRAGEN result bundles, run the automation script with input bundle and output report directories. It discovers export folders, parses SampleSheets and QC metrics, and normalizes them for downstream analysis.

Can I enrich genomics metadata using Illumina Connected Analytics?▼

Yes, you can enrich genomics metadata using Illumina Connected Analytics by supplying an optional ICA API key. The import process automatically fetches and integrates additional metadata during bundle processing.

What is needed to automate parsing of SampleSheets and QC metrics from DRAGEN exports?▼

Automating SampleSheet and QC metric parsing requires Python and the requests library. An optional ICA API key is needed if you want to enrich the normalized metadata using Illumina Connected Analytics.

Does this approach support routing reproducibility artifacts to downstream bioinformatics pipelines?▼

Yes, the import process supports routing reproducibility artifacts to downstream bioinformatics pipelines by generating manifests, writing reports, and suggesting appropriate next analysis steps.

What is the best way to handle VCFs and SampleSheets from DRAGEN export folders?▼

The best way to handle VCFs and SampleSheets from DRAGEN export folders is using an automated bridge script that parses them into a stable format and writes reproducibility manifests for local-first ecosystems.

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