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 exon-research/genomi --skill active-genome-indexgit clone --depth 1 https://github.com/exon-research/genomiWrote 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/exon-research/genomi/active-genome-index)<a href="https://agentmods.dev/skills/exon-research/genomi/active-genome-index"><img src="https://agentmods.dev/badge/skills/exon-research/genomi/active-genome-index/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/exon-research/genomi/active-genome-index"><img src="https://agentmods.dev/badge/skills/exon-research/genomi/active-genome-index.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00107 | $0.03756 |
| Opus 5 | $0.00053 | $0.01878 |
| Sonnet 5 | $0.00021 | $0.00751 |
| Haiku 4.5 | $0.00011 | $0.00376 |
Grade A, and why
active-genome-index 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 12d 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.
How it starts
The opening of the file, as written. The whole thing — 314 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Active Genome Index
Use this skill when the user provides a genome result file, asks to parse a genome source, asks what local Active Genome Index context exists, or asks a sample-specific question that requires a user file.
Goal
Create or refresh the private Active Genome Index and local evidence stores. Interpret health meaning only after the relevant evidence skill gathers support for the user's claim.
Convention: See
skills/conventions/context-routing.md. Convention: Seeskills/_output-rules.md.
Contract
Contract:
- A supplied source file or an Active Genome Index explicitly approved in the current session is accessible before sample-specific work.
GENOMI_HOMEstores durable Active Genome Index records.- Every genome source parsed by Genomi becomes an Active Genome Index record.
- User/profile nicknames belong to users, not genome artifacts.
- A user can have multiple genome records and one selected Active Genome Index.
- A default user is auto-selected as metadata for every session using this
GENOMI_HOME; its selected Active Genome Index still requires current-session approval before a private read. genomi.parse_sourcedigitizes the intake file so future inquiries use the Active Genome Index.- The original intake path is hidden from normal agent-facing context after parsing.
- Parsing success creates a source-appropriate Active Genome Index for later interpretation.
Supported Sources
- VCF/gVCF: variant callsets with VCF records, genotype fields, optional depth/quality, and possible region callability.
- BAM: aligned sequencing reads. Genomi derives a local VCF from the reads with a matching reference FASTA, then builds an Active Genome Index for the derived callset for normal sample-specific tools.
- FASTQ (paired-end): raw reads from sequencing services such as Nebula, Dante Labs, and Sequencing.com. Genomi auto-detects the R2 sibling, picks minimap2 (long reads) or bwa-mem2 (short reads) by the median sniffed read length, sorts the aligned BAM with samtools, then hands the BAM off to the standard BAM → derived-VCF path. Requires the
wgs-alignmentinstall purpose (or aligner binaries on PATH); a missing aligner returnsrequires_library_installinstead of failing. - 23andMe raw genotype text or zip/tar archive: consumer SNP-array calls with
rsid, chromosome, position, and plus-strand genotype on GRCh37. - genome.computer
.genome/1.0bundle directory or archive withmanifest.json,schema.json, and partitionedvariants.parquetrecords. - AncestryDNA raw genotype text or zip/tar archive: consumer SNP-array calls with
rsid, chromosome, position,allele1, andallele2on GRCh37/build 37.1. - MyHeritage raw genotype CSV or zip/tar archive: comma-delimited
RSID,CHROMOSOME,POSITION,RESULTexports prefixed with a# MyHeritage DNA raw databanner, GRCh37. - FamilyTreeDNA Family Finder autosomal CSV or compressed/zip/tar archive: same
RSID,CHROMOSOME,POSITION,RESULTcolumns as MyHeritage but with no banner, build encoded in the filename (_o37_), GRCh37. - Living DNA autosomal text or zip/tar archive: tab-separated
rsid/chromosome/position/genotyperows with a# Living DNA customer genotype databanner on GRCh37.
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.
- 12d ago First seen · 314 lines · 107 tokens per session scan A 849102495d9b
active-genome-index is a skill published in the GitHub repository exon-research/genomi (482 stars, last pushed 10d ago), licensed Apache-2.0. It adds 107 tokens to every session and 3,756 once invoked, about $0.0005 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 2026-08-30.
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