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-duplicate-handlinggit 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-duplicate-handling)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-duplicate-handling"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-duplicate-handling/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-duplicate-handling"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-duplicate-handling.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 | $0.00039 | $0.04189 |
| Opus 5 | $0.00019 | $0.02094 |
| Sonnet 5 | $0.00008 | $0.00838 |
| Haiku 4.5 | $0.00004 | $0.00419 |
Grade A, and why
bio-duplicate-handling 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
98% identical to bio-duplicate-handling — 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 — 379 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: picard 3.1+, pysam 0.22+, samtools 1.19+
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.
Duplicate Handling
"Remove PCR duplicates from my BAM file" -> Mark or remove duplicate reads using the fixmate-sort-markdup pipeline to prevent duplicate bias in variant calling.
- CLI:
samtools fixmate,samtools markdup(samtools) - Python:
pysam.fixmate(),pysam.markdup()(pysam)
Mark and remove PCR/optical duplicates using samtools.
Why Remove Duplicates?
PCR duplicates are identical copies of the same original molecule, created during library preparation. They inflate coverage, bias allele frequencies, and create false positive variant calls. Optical duplicates are flowcell-proximity artifacts: on unpatterned flowcells they arise when the imaging software splits one cluster into two adjacent calls; on patterned flowcells (NovaSeq, NovaSeq X, NextSeq 1000/2000, HiSeq X/4000) the dominant source is ExAmp (exclusion-amplification) "pad-hopping", where a library molecule re-seeds a nearby nanowell.
When to Mark Duplicates -- and When NOT To
Standard samtools markdup is the right tool for some assays and actively harmful for others. The decision is assay-driven:
| Assay | Standard markdup? | Recommended approach |
|---|---|---|
| Germline WGS / WES (PCR or PCR-free) | YES | samtools markdup (PCR-free still has ~0.5% optical duplicates on patterned flowcells) |
| Somatic tumor/normal (no UMI) | YES | Same |
| Exome / target capture | YES (20-50% expected) | samtools markdup |
| ChIP-seq | MARK, do not remove | Then use peak caller's auto-dup logic (macs3 --keep-dup auto) |
| CUT&RUN / CUT&Tag | MARK, do not remove | Same |
| ATAC-seq | YES, BEFORE Tn5 +4/-5 shift | Then shift coords for footprinting |
| Bulk RNA-seq (no UMIs) | NO | Duplicates are biological at highly-expressed loci; removing them biases DE proportional to expression |
| Bulk RNA-seq (with UMIs) | NO | umi_tools dedup |
| scRNA (10x, STARsolo, drop-seq) | NO | umi_tools dedup with CB+UB tags, or rely on Cell Ranger UMI counts |
| ctDNA / liquid biopsy / deep panel (UMI) | NO | fgbio GroupReadsByUmi -> CallDuplexConsensusReads |
| Twist / IDT / Roche UMI capture | NO | fgbio or Picard UmiAwareMarkDuplicatesWithMateCigar |
| Amplicon / hotspot panel (no UMI) | NO | Every read is a "duplicate" by coordinate; markdup erases the dataset. Use samtools ampliconclip instead -- see alignment-amplicon-clipping. |
| Amplicon / hotspot panel (UMI) | NO | fgbio consensus |
| Long-read native (ONT, PacBio HiFi unamplified) | NO | No PCR step; markdup is meaningless |
| PacBio HiFi amplicon | YES (rare) | pbmarkdup |
| Ancient DNA (aDNA) | YES + mapDamage | Run markdup, then mapDamage --rescale before variant calling |
| Microbiome 16S/ITS | NO | Read counts encode community structure |
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 · 379 lines · 39 tokens per session scan A 7ef875ece70c
bio-duplicate-handling is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 39 tokens to every session and 4,189 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. It is 98% identical to bio-duplicate-handling, differing in 12 lines, and is treated as a copy.
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