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LLMs-Universal-Life-Science-and-Clinical-Skills- Connected_Multiomics

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T=$(mktemp -d) && git clone --depth=1 https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- "$T" && mkdir -p ~/.claude/skills && cp -r "$T/Skills/Multi_Omics/Connected_Multiomics" ~/.claude/skills/mdbabumiamssm-llms-universal-life-science-and-clinical-skills-connected-multiomi && rm -rf "$T"
manifest: Skills/Multi_Omics/Connected_Multiomics/SKILL.md
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name: illumina-connected-multiomics description: Operate Illumina's Connected Multiomics SaaS to orchestrate tertiary analysis across single-cell, spatial, proteomic, methylation, and bulk omics with DRAGEN integration. keywords:

  • multi-omics
  • illumina
  • spatial-transcriptomics
  • methylation
  • tertiary-analysis measurable_outcome: Build a study, ingest DRAGEN outputs, and publish a multi-layer dashboard (cells + spatial + methylation) for collaborators within one day. license: Proprietary (Illumina Connected Software) metadata: author: Multi-Omics Integration Guild version: "2026.03" compatibility:
  • system: Illumina Connected Multiomics (cloud) allowed-tools:
  • web_fetch
  • read_file

Illumina Connected Multiomics Skill

Use this skill to standardize tertiary analysis when your lab already relies on Illumina prep kits, NextSeq/NovaSeq data, or DRAGEN pipelines and wants to avoid stitching dozens of open-source notebooks.

Why This Platform

  • Integrated modalities: single-cell RNA, spatial transcriptomics, proteomics, methylation, miRNA, and genome layers in one UI.
  • Sample-to-insight workflows: ingest DRAGEN secondary outputs directly, configure analysis templates, and generate publication-ready figures.
  • Secure SaaS: multi-tenant cloud with domain/workgroup isolation, aligning with regulated lab needs.

Setup Checklist

  1. Register domain & workgroup via Connected Software console; assign admins with SSO (SAML/OAuth).
  2. Connect data sources:
    • DRAGEN S3 buckets or BaseSpace Sequence Hub projects.
    • Uploads from local storage (FASTQ, processed counts, proteomics matrices).
  3. Provision roles: Biologist (read/analyze) vs Bioinformatician (template editing). Map to Illumina user groups.
  4. Whitelabel compliance: enable audit logging plus IP allowlists if PHI/clinical data is involved.

Standard Workflow

  1. Create Study: define cohorts, metadata schema, and modality checkboxes (RNA, spatial, methylation) inside the Study Builder.
  2. Load Data:
    • Use 
      Add Data → DRAGEN
      to pull secondary outputs.
    • For third-party assays, choose 
      Custom Matrix
      and map gene/protein identifiers.
  3. Run Pipelines: pick from preconfigured workflows (single-cell clustering, spatial DE, 5-base methylation). Parameter editor exposes filters, clustering resolution, and reference ontologies.
  4. Interpretation Layer:
    • Use interactive embeddings to gate clusters, show tissue overlays, or compute DMRs.
    • Link results to curated knowledge bases (cell type atlases, pathways) via built-in Correlation Engine connectors.
  5. Share Dashboards: publish read-only views or export high-res plots; optionally push to Connected Insights for downstream teams.

Tips & Guardrails

  • Version control templates: duplicate Illumina defaults before editing so upgrades do not overwrite them.
  • Capture provenance by locking workflow parameter JSON; attach to ELN or LIMS entries.
  • For large studies, enable cold storage tiering so archived runs do not impact subscription limits.
  • Use Connected Analytics if you need notebook-level custom analyses; embed outputs back into Multiomics studies for visualization.

References

  1. Illumina, Connected Multiomics product page – modality coverage and visualization features. https://www.illumina.com/products/by-type/informatics-products/connected-multiomics.html
  2. Illumina Developer Portal, Connected Multiomics release announcement (Jan 2026). https://developer.illumina.com/news-updates/unlock-deeper-multiomic-insights-with-illumina-connected-multiomics
  3. Illumina Connected Software Docs, Domain/workgroup setup for Connected Multiomics. https://help.connected.illumina.com/multiomics-software/connected-multiomics
  4. Illumina Connected Software Docs, About Connected Multiomics. https://help.connected.illumina.com/icm
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