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 agentmods add skills/gptomics/bioskills/alignment-validationnpx skills add GPTomics/bioSkills --skill alignment-validationgit clone --depth 1 https://github.com/GPTomics/bioSkillsWhat 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 | $0.00043 | $0.04213 |
| Opus 5 | $0.00022 | $0.02107 |
| Sonnet 5 | $0.00009 | $0.00843 |
| Haiku 4.5 | $0.00004 | $0.00421 |
Grade A, and why
bio-alignment-validation 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 yesterday.
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-alignment-validation — 92% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 398 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, 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.
Alignment Validation
Post-alignment quality control to verify alignment quality and identify issues.
"Check alignment quality" -> Compute post-alignment QC metrics (mapping rate, pairing, insert size, strand balance) to identify issues before downstream analysis.
- CLI:
samtools flagstat,samtools stats, PicardCollectAlignmentSummaryMetrics - Python:
pysam.AlignmentFileiteration with metric calculations
Two Different Validations
| Concern | Tools | What it catches |
|---|---|---|
| File integrity | samtools quickcheck, picard ValidateSamFile |
Truncation, missing EOF, malformed records, wrong CIGAR, MAPQ out of range |
| Sequence dictionary identity | samtools dict + M5 diff |
BAM aligned to wrong reference flavor / different decoy / chr vs no-chr |
| QC metrics | samtools stats, flagstat, mosdepth, Picard CollectMultipleMetrics / CollectHsMetrics / CollectWgsMetrics |
Are the data biologically reasonable for the assay? |
| Contamination / sample swap | verifybamid2, somalier, Picard CrosscheckFingerprints |
Cross-sample contamination, tumor-normal swap, mislabeled sample |
A file can pass quickcheck and still be malformed in ways that crash GATK three hours into HaplotypeCaller. Conversely, a QC-poor BAM can be structurally valid.
File Integrity
# Fast: header + EOF block check (misses mid-file truncation, invalid CIGAR)
samtools quickcheck -v in.bam || echo "QUICKCHECK FAILED"
samtools quickcheck -v *.bam > bad_bams.fofn # one fail-line per bad file
# Slow but thorough: structural validation
picard ValidateSamFile I=in.bam MODE=SUMMARY R=ref.fa
# Production: ignore expected-but-noisy
picard ValidateSamFile I=in.bam MODE=SUMMARY R=ref.fa \
IGNORE=INVALID_MAPPING_QUALITY \
IGNORE=MISMATCH_FLAG_MATE_NEG_STRAND
What ships with it
3 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.
- yesterday First seen · 398 lines · 43 tokens per session scan A 748b149783ea
bio-alignment-validation is a skill published in the GitHub repository GPTomics/bioSkills (1,198 stars, last pushed 16d ago), licensed MIT. It adds 43 tokens to every session and 4,213 once invoked, about $0.0002 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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