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discovery-d1-pangenome

Discovery D1: pangenome ecosystem + Garrison lab roadmap

Metadata

Statusdone
Assignedagent-128
Agent identityf51439356729d112a6c404803d88015d5b44832c6c584c62b96732b63c2b0c7e
Created2026-05-01T22:55:42.029857902+00:00
Started2026-05-01T22:59:39.762305003+00:00
Completed2026-05-01T23:07:26.454225061+00:00
Tagsgrant,urgent,v3,discovery, eval-scheduled
Eval score0.93
└ blocking impact0.92
└ completeness0.95
└ constraint fidelity0.85
└ coordination overhead0.93
└ correctness0.92
└ downstream usability0.94
└ efficiency0.90
└ intent fidelity0.86
└ style adherence0.93

Description

Description

Identify NAMED, ONGOING bioinformatics work in the pangenome ecosystem that the Garrison lab is leading or substantially contributing to, suitable for citing as concrete deliverables in v3.1's §17 / §19 / §43-§46 / §28. Goal: replace v3's vague 'longitudinal deployment in founders' active research' with named software, named papers in progress, named consortium contributions.

This addresses panel weakness W1 (no specific science deliverable) and W7 (authority borrowed, not tied to deliverable).

What to research

Use WebFetch / WebSearch. Cite URLs. If a source is unavailable, say so.

  1. github.com/pangenome — the Pangenomics organization. Survey active repos, recent commits, who's contributing. Identify projects under active development.
  2. github.com/vgteam — the vg organization. Same.
  3. github.com/pangenome/pggb — PGGB itself, recent activity.
  4. HPRC (humanpangenome.org) — what's the current roadmap? What's coming in the next 36 months for the human pangenome reference?
  5. Garrison lab recent publications — preprints on bioRxiv, recent Nature / Nat Methods / Nat Biotech publications, anything in submission. Search 'erik garrison pangenome 2025 2026'.
  6. Garrison's UTHSC lab page if findable.
  7. Cross-reference: which projects have Garrison or named lab members as active maintainers / first authors / corresponding authors?

What to produce

~/poietic.life/notes/v3-discovery-d1-pangenome-ecosystem-20260501.md — under 1200 words, structured as:

Active named software with ongoing development

For each: name, repo URL, current status (alpha / beta / production), what it does in one sentence, whether Garrison lab leads or contributes, and whether it could plausibly be a v3.1 deliverable.

Papers in progress / recent

For each: title (or topic if untitled), venue (or 'preprint pending'), URL if available, Garrison's role, expected timeline.

HPRC roadmap items

What does HPRC plan to deliver over the next 36 months that Garrison's lab is positioned to contribute? Be specific.

Pangenome group active research arcs

Beyond software, what scientific questions are being actively pursued in the pangenome ecosystem? Cite people and groups.

Recommended named deliverables for v3.1

3-5 specific deliverables (with named software / paper / dataset) that v3.1 could cite under §43-§46 milestones. For each, the month-X timing claim that's defensible.

Constraints

  • Cite URLs for every factual claim.
  • Distinguish 'Garrison lab leads' from 'Garrison contributes' from 'pangenome group, Garrison adjacent.' Each is fine as a v3 reference but the framing differs.
  • Do NOT invent. If you can't verify a project is active, say so.
  • No em-dashes.

Validation

  • github.com/pangenome surveyed with recent activity noted
  • github.com/vgteam surveyed
  • HPRC roadmap researched
  • Garrison's recent (2025-2026) publication trail mapped
  • At least 5 named active projects with verified Garrison involvement
  • At least 3 recommended named deliverables for v3.1
  • URLs cited throughout
  • Output at ~/poietic.life/notes/v3-discovery-d1-pangenome-ecosystem-YYYYMMDD.md

Depends on

Required by

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