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 bin-level-sequencing-depth-calculationgit 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/bin-level-sequencing-depth-calculation)<a href="https://agentmods.dev/skills/holobiomicslab/asb-skill-collections/bin-level-sequencing-depth-calculation"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/bin-level-sequencing-depth-calculation/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/bin-level-sequencing-depth-calculation"><img src="https://agentmods.dev/badge/skills/holobiomicslab/asb-skill-collections/bin-level-sequencing-depth-calculation.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 | $0.00068 | $0.01431 |
| Opus 5 | $0.00034 | $0.00715 |
| Sonnet 5 | $0.00014 | $0.00286 |
| Haiku 4.5 | $0.00007 | $0.00143 |
Grade A, and why
bin-level-sequencing-depth-calculation 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 10d 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.
bin-level-sequencing-depth-calculation
Summary
Compute per-bin sequencing depth (coverage) from a cooler Hi-C contact matrix using cooltools.coverage(), producing a bedGraph or tabular track of read counts per genomic bin. This enables quality assessment and normalization of high-resolution chromosome conformation capture datasets.
When to use
You have a cooler file (.cool or .mcool) from a Hi-C or micro-C experiment and need to quantify the total number of sequencing reads assigned to each genomic bin to assess coverage uniformity, identify poorly-sequenced regions, or prepare bin-level weights for downstream normalization. Specifically useful when the cooler object is already loaded in memory and you want to export coverage as a track file (bedGraph or tabular CSV/TSV).
When NOT to use
- Input data is already a normalized or log-transformed contact matrix (coverage calculation assumes raw counts).
- You need trans (inter-chromosomal) coverage only; cooltools.coverage() by default computes cis (intra-chromosomal) counts.
- The cooler file has no valid bin or contact data (e.g., empty or corrupted cooler).
Inputs
- cooler contact matrix object (loaded via cooler.Cooler() or cooler.open_cooler())
- Hi-C or micro-C cooler file (.cool or .mcool format)
Outputs
- bedGraph file or tabular track (CSV/TSV) with columns: chromosome, start, end, coverage
- optionally, cis count column stored in cooler HDF5 metadata
How to apply
Load a cooler contact matrix object using the cooler library, then call cooltools.coverage() on it to compute per-bin sequencing depth. The function signature permits optionally storing total cis counts as a new column in the cooler HDF5 file. After computation, export the resulting coverage array (bin coordinates + coverage values) to bedGraph or tabular format (CSV/TSV). Validate the output by checking that the number of rows matches the total bin count in the cooler object's bins table, and that coverage values are non-negative integers or floats reflecting read accumulation per bin.
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.
- 10d ago First seen · 97 lines · 68 tokens per session scan A e2e21e5d485d
bin-level-sequencing-depth-calculation is a skill published in the GitHub repository HolobiomicsLab/asb-skill-collections (15 stars, last pushed 4d ago), licensed Apache-2.0. It adds 68 tokens to every session and 1,431 once invoked, about $0.0003 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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