discovery-d3-cnv — Workgraph

Metadata

Status	done
Assigned	`agent-126`
Agent identity	`8da3b6fc81685ca44a4e15eb35307ab90ce3f0500e9c08b8b0caae848f7d4ce9`
Created	2026-05-01T22:56:12.522124482+00:00
Started	2026-05-01T22:58:34.481200490+00:00
Completed	2026-05-01T23:02:06.339084288+00:00
Tags	`grant,urgent,v3,discovery`, `eval-scheduled`
Eval score	0.83
└ blocking impact	0.95
└ completeness	0.95
└ coordination overhead	0.95
└ correctness	0.90
└ downstream usability	0.92
└ efficiency	0.90
└ intent fidelity	0.85
└ style adherence	0.95

Description

Erik specifically flagged 'CNV-aware aligners and all this kind of stuff' as part of the ongoing methods-development arc that WorkGraph would substrate. Identify the named tools, methods papers, and aligner-development projects in motion in the Garrison lab and pangenome ecosystem. Goal: v3.1 §43-§46 cites named methods-development deliverables.

Addresses panel weakness W4 (milestones vague) — replace 'methodology paper drafted as preprint' with named tools/methods.

What to research

Use WebFetch / WebSearch.

CNV-aware alignment in pangenome context — what does this mean technically? Standard read aligners (BWA, minimap2) handle copy-number-variable regions poorly. Pangenome-aware aligners (vg map, vg giraffe) can do better but CNV-specific tooling is an active area. Identify projects.
vg / pangenome aligner ecosystem — recent developments, what's in active development. github.com/vgteam, github.com/pangenome.
Erik's recent methods development — preprints / papers from 2024-2026 on aligners, variant callers, graph construction. bioRxiv search 'erik garrison aligner', 'erik garrison variant calling pangenome'.
Other pangenome methods development — odgi, seqwish, smoothxg evolution. Anything new in the pipeline.
Cross-reference — which methods are positioned for development under WorkGraph coordination?

What to produce

~/poietic.life/notes/v3-discovery-d3-cnv-methods-20260501.md — under 1000 words.

Structure:

CNV-aware alignment: state of the field

One paragraph technical summary. What's the gap? What works? What doesn't?

Active named methods-development projects

For each: name, repo, status, who leads, what it does, why it matters.

Erik's recent methods work

Cite preprints / papers from 2024-2026 on methods development.

Named v3.1 deliverables

3-5 specific methods-development deliverables (named tool / named paper / named workshop output) suitable for v3.1 §43-§46 milestones. With timing.

WorkGraph's substrate role for methods development

Why does coordination of methods-development across multiple contributors benefit from WorkGraph specifically? Be concrete.

Constraints

Cite URLs.
Distinguish 'Garrison leads' vs 'Garrison contributes.'
No em-dashes.

Validation

CNV-aware alignment field summarized with citations
At least 3 named active methods-development projects
Erik's recent methods publications cited
At least 3 named v3.1 deliverables proposed
WorkGraph substrate role articulated
Output at ~/poietic.life/notes/v3-discovery-d3-cnv-methods-YYYYMMDD.md

## Description

Erik specifically flagged 'CNV-aware aligners and all this kind of stuff' as part of the ongoing methods-development arc that WorkGraph would substrate. Identify the named tools, methods papers, and aligner-development projects in motion in the Garrison lab and pangenome ecosystem. Goal: v3.1 §43-§46 cites named methods-development deliverables.

Addresses panel weakness W4 (milestones vague) — replace 'methodology paper drafted as preprint' with named tools/methods.

## What to research

Use WebFetch / WebSearch.

1. **CNV-aware alignment in pangenome context** — what does this mean technically? Standard read aligners (BWA, minimap2) handle copy-number-variable regions poorly. Pangenome-aware aligners (vg map, vg giraffe) can do better but CNV-specific tooling is an active area. Identify projects.
2. **vg / pangenome aligner ecosystem** — recent developments, what's in active development. github.com/vgteam, github.com/pangenome.
3. **Erik's recent methods development** — preprints / papers from 2024-2026 on aligners, variant callers, graph construction. bioRxiv search 'erik garrison aligner', 'erik garrison variant calling pangenome'.
4. **Other pangenome methods development** — odgi, seqwish, smoothxg evolution. Anything new in the pipeline.
5. **Cross-reference** — which methods are positioned for development under WorkGraph coordination?

## What to produce

`~/poietic.life/notes/v3-discovery-d3-cnv-methods-20260501.md` — under 1000 words.

Structure:

### CNV-aware alignment: state of the field
One paragraph technical summary. What's the gap? What works? What doesn't?

### Active named methods-development projects
For each: name, repo, status, who leads, what it does, why it matters.

### Erik's recent methods work
Cite preprints / papers from 2024-2026 on methods development.

### Named v3.1 deliverables
3-5 specific methods-development deliverables (named tool / named paper / named workshop output) suitable for v3.1 §43-§46 milestones. With timing.

### WorkGraph's substrate role for methods development
Why does coordination of methods-development across multiple contributors benefit from WorkGraph specifically? Be concrete.

## Constraints

- Cite URLs.
- Distinguish 'Garrison leads' vs 'Garrison contributes.'
- No em-dashes.

## Validation
- [ ] CNV-aware alignment field summarized with citations
- [ ] At least 3 named active methods-development projects
- [ ] Erik's recent methods publications cited
- [ ] At least 3 named v3.1 deliverables proposed
- [ ] WorkGraph substrate role articulated
- [ ] Output at `~/poietic.life/notes/v3-discovery-d3-cnv-methods-YYYYMMDD.md`

Depends on

done .assign-discovery-d3-cnv

Required by

Log

2026-05-01T22:56:12.519506362+00:00 Task paused
2026-05-01T22:58:08.120063145+00:00 Task published
2026-05-01T22:58:34.058720036+00:00 Lightweight assignment: agent=Default Documenter (8da3b6fc), exec_mode=full, context_scope=task, reason=Documenter role optimized for research synthesis and structured markdown creation; full mode required to write output file.
2026-05-01T22:58:34.481204698+00:00 Spawned by coordinator --executor claude --model opus
2026-05-01T22:59:00.412653851+00:00 Starting research on CNV-aware aligners and pangenome methods development for v3.1 §43-§46
2026-05-01T23:00:36.721335119+00:00 Research complete: identified vg giraffe, wfmash, impg, COSIGT, adaptive tracepoints, ctyper, PGGB, MemPanG26, sweepga, PanVariants, HPRCv2 as active methods-development projects. Drafting note.
2026-05-01T23:01:59.493857301+00:00 Committed: f00316e in poietic.life. Note: 953 words, no em-dashes, all 6 validation items met. Not pushing (branch diverged with remote — leaving rebase decision to graph owner).
2026-05-01T23:02:06.339091712+00:00 Task pending eval (agent reported done; awaiting `.evaluate-*` to score)
2026-05-01T23:04:49.087459575+00:00 PendingEval → Done (evaluator passed; downstream unblocks)