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 clip-alignmentgit 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/clip-alignment)<a href="https://agentmods.dev/skills/gptomics/bioskills/clip-alignment"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/clip-alignment/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/clip-alignment"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/clip-alignment.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 | $0.00117 | $0.05638 |
| Opus 5 | $0.00059 | $0.02819 |
| Sonnet 5 | $0.00023 | $0.01128 |
| Haiku 4.5 | $0.00012 | $0.00564 |
Grade A, and why
bio-clip-seq-clip-alignment 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-clip-seq-clip-alignment — 98% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 296 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: STAR 2.7.11b+, bowtie2 2.5.3+, HISAT2 2.2.1+, samtools 1.19+, CLAM 1.2+, umi_tools 1.1.5+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws unexpected errors, introspect the installed binary (<tool> -h) and adapt the example to match the actual CLI rather than retrying.
CLIP-seq Alignment
"Align preprocessed CLIP reads to genome with crosslink-preserving parameters" -> Map UMI-extracted, adapter-trimmed reads to the genome (NOT transcriptome) with end-to-end alignment, strict mismatch ceiling, and unique-mapper-only filtering by default. The 5' end of the read (R2 5' in paired-end eCLIP; R1 5' in iCLIP) carries the reverse-transcriptase truncation = crosslink site -1; any soft-clipping or 5' trimming during alignment destroys nucleotide resolution.
- CLI (eCLIP / iCLIP / iCLIP2, ENCODE pattern):
STAR --runMode alignReads --genomeDir STAR_index --readFilesIn R1.trim.fq.gz R2.trim.fq.gz --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMismatchNoverReadLmax 0.04 --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outFileNamePrefix sample_ - CLI (PAR-CLIP, mismatch ceiling raised for T->C signal): same as above but
--outFilterMismatchNoverReadLmax 0.07 - CLI (low memory, no splicing):
bowtie2 -x genome_index -U R1.trim.fq.gz --very-sensitive -p 8 | samtools view -bS - | samtools sort -o aligned.bam - CLI (repeat-binding RBP, multi-mapper rescue):
STAR ... --outFilterMultimapNmax 100 --outSAMmultNmax -1then process withCLAM(see repeat-element section)
End-to-end alignment is non-negotiable. --alignEndsType Local (STAR default for some pipelines) soft-clips low-quality 5' bases and discards exactly the truncation signal. Mismatch ceiling 0.04 (4% of read length) excludes most sequencing-error reads; 0.07 is the PAR-CLIP override to retain T->C reads.
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 · 296 lines · 117 tokens per session scan A 4895f2e540ba
bio-clip-seq-clip-alignment is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 117 tokens to every session and 5,638 once invoked, about $0.0006 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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