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 alignment-validationgit 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/alignment-validation)<a href="https://agentmods.dev/skills/gptomics/bioskills/alignment-validation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/alignment-validation/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/alignment-validation"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/alignment-validation.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 | $0.00043 | $0.04213 |
| Opus 5.5 | $0.00017 | $0.01685 |
| Sonnet 5.5 | $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 1mo 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-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.
- 1mo ago First seen · 398 lines · 43 tokens per session scan A 748b149783ea
bio-alignment-validation is a skill published in the GitHub repository GPTomics/bioSkills (1,223 stars, last pushed 2mo ago), licensed MIT. It adds 43 tokens to every session and 4,213 once invoked, about $0.0002 per session on Opus 5.5. 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.
Other skills, from other repositories
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full…
exploratory-data-analysis
Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain…
matlab
Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data, tests, projects, graphics, MAT files, and explicit Python interoperability.
phylogenetics
Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein…
research-engineer
An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology.
presenting-conference-talks
Generates conference presentation slides (Beamer LaTeX PDF and editable PPTX) from a compiled paper with speaker notes and talk script. Use when preparing oral talks, spotlight presentations, or invited talks for ML and systems conferences.