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 PKU-YuanGroup/OpenAI4S --skill bio-alignment-files-alignment-amplicon-clippinggit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-alignment-files-alignment-amplicon-clipping)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-amplicon-clipping"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-amplicon-clipping/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/pku-yuangroup/openai4s/bio-alignment-files-alignment-amplicon-clipping"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-alignment-amplicon-clipping.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 | $0.00071 | $0.02443 |
| Opus 5 | $0.00036 | $0.01222 |
| Sonnet 5 | $0.00014 | $0.00489 |
| Haiku 4.5 | $0.00007 | $0.00244 |
Grade A, and why
bio-alignment-amplicon-clipping 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.
This is a copy
95% identical to bio-alignment-amplicon-clipping — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 167 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: samtools 1.19+, pysam 0.22+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Alignment Amplicon Clipping
"Trim primer-derived bases from amplicon BAM" -> Soft- or hard-clip the 5' primer footprint after alignment using a primer BED, then repair fixmate/MD/NM tags.
- CLI:
samtools ampliconclip -b primers.bed input.bam -o clipped.bam(since samtools 1.11) - Alternative:
iVar trim,BAMClipper,fgbio ClipBam
Why Primer Trimming After Alignment
Amplicon panels (SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, fusion panels, 16S rRNA) use designed PCR primers for enrichment. Primer-derived bases at read 5' ends do NOT reflect biological sequence -- they reflect the primer template. Without trimming:
- False reference confirmation at primer footprint positions.
- Variant allele frequency suppressed at variants under primers (the primer sequence cannot capture the variant base).
- Strand bias artifacts (primers are typically one-strand).
Standard amplicon BAMs should NEVER be processed by samtools markdup -- by design every read at a primer location is a "duplicate" by coordinate. See duplicate-handling for the assay-aware decision.
Tool Selection
| Tool | When | Notes |
|---|---|---|
samtools ampliconclip |
Default for amplicon panels (since 1.11) | Soft- or hard-clip from BED; modifies CIGAR; invalidates MD/NM |
iVar trim |
Illumina SARS-CoV-2 / PrimalSeq route (Andersen lab) | Coordinates by primer name/position; soft-clips only + quality sliding-window |
BAMClipper |
Capture / hybrid panels with primer overlap | 5'-end clipping with overlap handling |
fgbio ClipBam |
When read-pair coordination matters | Soft/hard-clip with mate-aware end adjustment |
cutadapt (pre-alignment) |
Legacy / when alignment is downstream | Trims at FASTQ stage; less precise for amplicon |
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.
- 12d ago First seen · 167 lines · 71 tokens per session scan A 0f46a3c50274
bio-alignment-amplicon-clipping is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed today), licensed MIT. It adds 71 tokens to every session and 2,443 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-alignment-amplicon-clipping, differing in 12 lines, and is treated as a copy.
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