bio-longread-alignment
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use…
Maintainer Lylll9436 · Last updated April 1, 2026
Scan an experiment repo and generate a complete paper outline (H1/H2/H3) with user approval checkpoints at each level, then generate body text with evidence annotations, citations, and bilingual output. Python ML repos. 扫描实验仓库,逐级生成论文大纲(H1/H2/H3),每级用户确认后推进, 然后生成带证据标注、引用和双语输出的正文文本。.
Original source
https://github.com/Lylll9436/Paper-Polish-Workflow-skill/tree/main/skills/ppw-repo-to-paper
Skill Snapshot
Source Doc
| Mode | Default | Behavior |
|---|---|---|
guided | Yes | Full 5-step workflow with confirmation at each heading level and section-by-section body generation |
direct | Not supported -- outline generation inherently requires user validation at each level | |
batch | Not supported -- each repo requires unique analysis |
Default mode: guided. The layered confirmation design is central to this Skill.
| File | Purpose |
|---|---|
references/repo-patterns.md | File categorization patterns and section mapping rules |
references/bilingual-output.md | Bilingual output format (Skill is bilingual-eligible) |
references/body-generation-rules.md | Anti-hallucination rules, citation integration, bilingual format, references.bib algorithm |
references/journals/ceus.md | CEUS journal formatting contract (writing style, section guidance) |
None. All reference files are in required because Step 5 body generation always needs CEUS formatting.
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