Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill pangenome-analysisgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/pangenome-analysis)<a href="https://agentmods.dev/skills/gptomics/bioskills/pangenome-analysis"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/pangenome-analysis/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/pangenome-analysis"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/pangenome-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00200 | $0.08887 |
| Opus 5 | $0.00100 | $0.04444 |
| Sonnet 5 | $0.00040 | $0.01777 |
| Haiku 4.5 | $0.00020 | $0.00889 |
Grade A, and why
bio-comparative-genomics-pangenome-analysis scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-comparative-genomics-pangenome-analysis — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 498 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: Panaroo 1.5.1+ (Tonkin-Hill 2020 Genome Biol 21:180), PPanGGOLiN 2.2.0+ (Gautreau 2020 PLoS Comp Biol 16:e1007732), PEPPAN 1.0.5+ (Zhou 2020 GR 30:1667), GET_HOMOLOGUES 25102023+, anvi'o 8.0+ (Eren 2021 Nat Microbiol 6:3), Minigraph-Cactus (Hickey 2024 Nat Biotech 42:663; bundled with Cactus 2.5+), PGGB 0.7.5+ (Garrison 2024 Nat Methods 21:2008), vg 1.59.0+ (Sirén J et al 2024 Nat Methods 21:2017), PanGenie 3.1.0+ (Ebler 2022 Nat Genet 54:518), PGR-TK 0.3.6+ (Chin 2023 Nat Methods 20:1213; cschin/pgr-tk; repo archived April 2026 transitioning to PANGEA), PANGEA (in development by DGI / Diploid Genomics as PGR-TK's successor for pangenome graph exploration + analysis -- check https://github.com/cschin/pgr-tk for current repository pointer), Bakta 1.10.4+ (annotation for input), Roary 3.13.0+ (DEPRECATED; use Panaroo), Scoary 1.6.16+, pyseer 1.3.11+, BUSCO 5.7+, FastTree 2.1.11+, RAxML-NG 1.2+. Python 3.10+ required for Panaroo / PPanGGOLiN.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
panaroo --version;ppanggolin --version;peppan --help;cactus-pangenome --help;pggb --version;vg version - Python:
pip show panaroo ppanggolin
If code throws Bakta annotation incompatible, GFA file inconsistent, vg index version mismatch, the bacterial pangenome ecosystem expects consistent annotation; re-annotate all input genomes with the same tool and version before pangenome analysis.
Pangenome Analysis
"What genes are universal vs accessory across this set of genomes?" -> The pangenome is the union of all genes across a sampled group; the Tettelin partition (Tettelin 2005 PNAS 102:13950) splits it into core (universal), shell (in many but not all), cloud (rare), and species-specific (private) genes. The fundamental dichotomy is bacterial pangenome (clusters genes into orthogroups; Panaroo / PPanGGOLiN / PEPPAN for compact genomes) vs eukaryotic pangenome (graph-based; Minigraph-Cactus / PGGB / vg for haplotype-resolved sequences). The choice depends on what's being represented: bacterial pangenome captures gene-content variation in a species/genus; eukaryotic pangenome graph captures haplotype-level structural and sequence variation. Roary (Page 2015) is now deprecated in favor of Panaroo, which handles annotation-error noise that previously inflated bacterial pangenomes substantially.
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 498 lines · 200 tokens per session scan A 3c346a7fe335
bio-comparative-genomics-pangenome-analysis is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 200 tokens to every session and 8,887 once invoked, about $0.0010 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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