lit-review-topic-11

Metadata

Status	abandoned
Agent identity	`3184716484e6f0ea08bb13539daf07686ee79d440505f1fdf2de0357707034c3`
Model	`codex:gpt-5.5`
Created	2026-05-06T01:43:35.028744197+00:00
Tags	`lit-review`, `eval-scheduled`
Failure reason	originally corrupted description; superseded by topic-11-2

Description

SHARED CONTEXT — Lit review fanout for the canonical Nature-format abstract (paper_prep/synthesis/ABSTRACT_nature.md, written by upstream task; falls back to ABSTRACT_BoG.md if Nature version not yet committed in your worktree). The deck/talk substrate is slides/v2/SLIDES_v2_PLAN.md + paper_prep/synthesis/CROSSWALK.md + end-to-end-report/. The author needs a chronologically structured, claim-anchored review per topic that pulls the field together so he can speak confidently in talk, Q&A, and during manuscript writing. OUTPUT FILES: paper_prep/lit_review/topic_NN_.md (1500-3000 words, chronological narrative tying each era`s key findings to claims C1-C8 of the abstract — be honest about which claims a reference supports vs only tangentially relates to) AND paper_prep/lit_review/topic_NN_.bib (BibTeX entries for new references this review introduces; do NOT duplicate entries already in paper_prep/synthesis/REFERENCES.bib — check first). USE WebSearch / WebFetch tools to find recent papers; combine with seed references provided per topic. SCOPE 10-30 references per topic (more for foundational topics, fewer for narrow ones). DO NOT write the manuscript itself; do NOT modify any other lit_review file; single commit per task: "docs: lit review topic NN — ".

THIS TOPIC (11): Pedigree-based variant and recombination detection — Cechova 2025 WashU 3-gen T2T pedigree; Porubsky 2025 CEPH1463 cross-assembler validation; de novo SVs/SNVs in trios; meiotic vs somatic distinction. Methods for distinguishing inherited variants from de novo events; cross-generation tracking. The methodological context for the abstracts companion paper, 466 haplotypes). Earlier population pangenome efforts: 1000 Genomes structural variants, gnomAD-SV, HGDP. Why HPRC v2 enables this paper specifically. The lineage of pangenome reference construction.

TIME RANGE: 2010-present (1000 Genomes era through HPRC v2).

SEED REFERENCES: Liao 2023 HPRC v1; 1000 Genomes structural variant papers; HPRC v2 (cite as 'in submission' / preprint if available). Find ~10-20 more on population pangenomics, reference-free assembly approaches, pangenome reference construction.

SHARED CONTEXT — Lit review fanout for the canonical Nature-format abstract (paper_prep/synthesis/ABSTRACT_nature.md, written by upstream task; falls back to ABSTRACT_BoG.md if Nature version not yet committed in your worktree). The deck/talk substrate is slides/v2/SLIDES_v2_PLAN.md + paper_prep/synthesis/CROSSWALK.md + end-to-end-report/. The author needs a chronologically structured, claim-anchored review per topic that pulls the field together so he can speak confidently in talk, Q&A, and during manuscript writing. OUTPUT FILES: paper_prep/lit_review/topic_NN_<slug>.md (1500-3000 words, chronological narrative tying each era`s key findings to claims C1-C8 of the abstract — be honest about which claims a reference supports vs only tangentially relates to) AND paper_prep/lit_review/topic_NN_<slug>.bib (BibTeX entries for new references this review introduces; do NOT duplicate entries already in paper_prep/synthesis/REFERENCES.bib — check first). USE WebSearch / WebFetch tools to find recent papers; combine with seed references provided per topic. SCOPE 10-30 references per topic (more for foundational topics, fewer for narrow ones). DO NOT write the manuscript itself; do NOT modify any other lit_review file; single commit per task: "docs: lit review topic NN — <slug>".

TIME RANGE: 2010-present (1000 Genomes era through HPRC v2).

Depends on

done update-abstract-rename

Required by

(none)

Log

2026-05-06T01:43:35.002321779+00:00 Task paused
2026-05-06T01:45:10.238393703+00:00 Task abandoned: description corrupted by bash quoting in dispatch script
2026-05-06T01:46:56.306756446+00:00 Task published
2026-05-06T02:20:02.145039070+00:00 reset via `wg reset lit-review-topic-01,lit-review-topic-02,lit-review-topic-04-2,lit-review-topic-05,lit-review-topic-06,lit-review-topic-07,lit-review-topic-08,lit-review-topic-09,lit-review-topic-10,lit-review-topic-12,lit-review-topic-13,lit-review-topic-14,lit-review-synthesis`; was Abandoned
2026-05-06T02:21:01.932529642+00:00 Task abandoned: originally corrupted description; superseded by topic-11-2