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 HolobiomicsLab/asb-skill-collections --skill hi-c-map-artifact-validationgit clone --depth 1 https://github.com/HolobiomicsLab/asb-skill-collectionsWrote 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/holobiomicslab/asb-skill-collections/hi-c-map-artifact-validation)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/hi-c-map-artifact-validation"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/hi-c-map-artifact-validation/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/holobiomicslab/asb-skill-collections/hi-c-map-artifact-validation"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/hi-c-map-artifact-validation.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 | $0.00049 | $0.01278 |
| Opus 5 | $0.00024 | $0.00639 |
| Sonnet 5 | $0.00010 | $0.00256 |
| Haiku 4.5 | $0.00005 | $0.00128 |
Grade A, and why
hi-c-map-artifact-validation 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.
How it starts
The opening of the file, as written. The whole thing — 97 lines — stays where its author put it; the contents beside it link to each section on GitHub.
hi-c-map-artifact-validation
Summary
Verification that a Juicer Hi-C processing pipeline has completed successfully and produced a valid .hic output file containing processed Hi-C contact map data. This skill ensures the pipeline's contact matrix construction, normalization, and artifact generation steps have executed correctly before downstream analysis.
When to use
After executing the Juicer pipeline on raw Hi-C FASTQ files, to confirm that the pipeline has generated the expected .hic output artifact and that the contact matrix construction and normalization steps completed without error.
When NOT to use
- Input data are already in .hic format (pre-processed contact maps)
- The pipeline stage parameter is set to 'early' (early exit requested)
- Raw FASTQ files have not yet been processed through the alignment and contact matrix construction stages
Inputs
- FASTQ raw Hi-C sequencing data files
- reference genome file
- restriction enzyme site file
- Juicer pipeline execution logs
Outputs
- .hic file (processed Hi-C contact map artifact)
- validation status report
- contact matrix statistics
How to apply
After the Juicer pipeline execution completes, verify the presence and integrity of the .hic output file in the designated output directory. Check that the pipeline's log files indicate successful completion of all stages: read alignment, contact matrix construction, and normalization. Confirm that the .hic file is a valid Java serialized object by attempting to load it with Juicer Tools' viewing or analysis commands. Validate that the contact matrix dimensions match the reference genome's chromosome structure and that normalized contact frequencies are present across expected resolution scales (kilobase resolution).
Related tools
- Juicer (Pipeline orchestration and Hi-C map generation from raw FASTQ data) — https://github.com/aidenlab/juicer
- Juicer Tools (Command-line utility for validating, viewing, and analyzing .hic contact map files) — https://github.com/aidenlab/juicer
- ENCODE Hi-C uniform processing pipeline (Cloud-based Juicer wrapper using Cromwell/Caper for production Hi-C processing) — https://github.com/ENCODE-DCC/hic-pipeline
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 · 97 lines · 49 tokens per session scan A 3afafee4cd0f
hi-c-map-artifact-validation is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 5d ago), licensed Apache-2.0. It adds 49 tokens to every session and 1,278 once invoked, about $0.0002 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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