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 atac-qcgit 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/atac-qc)<a href="https://agentmods.dev/skills/gptomics/bioskills/atac-qc"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/atac-qc/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/atac-qc"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/atac-qc.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 | $0.00096 | $0.05340 |
| Opus 5 | $0.00048 | $0.02670 |
| Sonnet 5 | $0.00019 | $0.01068 |
| Haiku 4.5 | $0.00010 | $0.00534 |
Grade A, and why
bio-atac-seq-atac-qc 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 9d 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-atac-seq-atac-qc — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 338 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: deepTools 3.5+, Picard 3.1+, samtools 1.19+, bedtools 2.31+, ATACseqQC 1.26+, pysam 0.22+, pyBigWig 0.3+, numpy 1.26+, pandas 2.2+, MultiQC 1.21+.
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - R:
packageVersion('<pkg>')then?function_nameto verify parameters - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt.
ATAC-seq Quality Control
"Does my ATAC library pass ENCODE quality criteria?" -> Compute the seven canonical metrics (depth, alignment rate, mitochondrial fraction, library complexity, fragment-size periodicity, TSS enrichment, FRiP) and compare against ENCODE 4 thresholds, then diagnose failures.
- CLI:
picard CollectInsertSizeMetrics,samtools flagstat,samtools idxstats - CLI:
deeptools plotFingerprint,computeMatrix reference-point+plotProfile - R:
ATACseqQC::TSSEscore,ATACseqQC::fragSizeDist,ATACseqQC::PTscore - Python: custom NRF/PBC from coordinate hash; pyBigWig for TSS enrichment
ENCODE 4 ATAC-seq Acceptance Thresholds
| Metric | Definition | Ideal | Acceptable | Reject | Source |
|---|---|---|---|---|---|
| Nuclear reads (after dedup, no chrM) | Mapped, MAPQ >= 30, non-chrM, deduped | >= 50M | 25-50M | < 25M | ENCODE 4 ATAC-seq Standards |
| Alignment rate | Mapped / total reads | >= 95% | 80-95% | < 80% | ENCODE 4 |
| Mitochondrial fraction | chrM / total mapped | < 5% (Omni-ATAC), < 20% (standard) | 20-50% | > 50% | Corces 2017 (Omni-ATAC) |
| NRF (Non-Redundant Fraction) | Distinct positions / total reads | >= 0.9 | 0.7-0.9 | < 0.7 | Landt 2012 |
| PBC1 (PCR Bottlenecking Coefficient 1) | Positions w/ 1 read / Positions w/ >= 1 read | >= 0.9 | 0.7-0.9 | < 0.7 | Landt 2012 |
| PBC2 | Positions w/ 1 read / Positions w/ 2 reads | >= 3.0 | 1.0-3.0 | < 1.0 | Landt 2012 |
| TSS enrichment (hg38, GENCODE v29) | Avg signal at TSS / avg flanking | >= 7 | 5-7 | < 5 | ENCODE 4 |
| FRiP (Fraction Reads in Peaks) | Reads in MACS peaks / total | >= 0.3 | 0.2-0.3 | < 0.2 | ENCODE 4, Landt 2012 |
| Insert-size periodicity | NFR + mono-nuc + di-nuc peaks visible | Clear 3+ peaks | NFR + mono only | Flat / single peak | Buenrostro 2013 |
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.
- 9d ago First seen · 338 lines · 96 tokens per session scan A ac0ae172d8d6
bio-atac-seq-atac-qc is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 25d ago), licensed MIT. It adds 96 tokens to every session and 5,340 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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