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/reference-operationsnpx skills add GPTomics/bioSkills --skill reference-operationsgit 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 | $0.00032 | $0.03321 |
| Opus 5 | $0.00016 | $0.01661 |
| Sonnet 5 | $0.00006 | $0.00664 |
| Haiku 4.5 | $0.00003 | $0.00332 |
Grade A, and why
bio-reference-operations scanned grade A with 1 finding 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 3d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
seq = ref.fetch(chrom) Copies of this mod
1 near-identical copy found in the catalogue:
- bio-reference-operations — 94% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 377 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: GATK 4.5+, bcftools 1.19+, 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.
Reference Operations
Generate consensus sequences and manage reference files using samtools.
"Prepare a reference genome" -> Index the FASTA and create a sequence dictionary for downstream tools.
- CLI:
samtools faidx ref.fa+samtools dict ref.fa -o ref.dict - Python:
pysam.FastaFile('ref.fa')(auto-uses .fai index)
"Build a consensus from BAM" -> Derive the most-supported base at each position from aligned reads.
- CLI:
samtools consensus input.bam -o consensus.fa - Python: iterate pileup columns and take majority base (pysam)
samtools faidx - Index Reference FASTA
Create index for random access to reference sequences.
Create Index
samtools faidx reference.fa
# Creates reference.fa.fai
Fetch Region from Reference
samtools faidx reference.fa chr1:1000-2000
Fetch Multiple Regions
samtools faidx reference.fa chr1:1000-2000 chr2:3000-4000
Fetch Entire Chromosome
samtools faidx reference.fa chr1
Output to File
samtools faidx reference.fa chr1:1000-2000 > region.fa
Reverse Complement
samtools faidx -i reference.fa chr1:1000-2000
FAI File Format
chr1 248956422 6 60 61
chr2 242193529 253105708 60 61
Columns: name, length, offset, line bases, line width
samtools dict - Create Sequence Dictionary
Create SAM header dictionary for reference (used by GATK, Picard).
Create Dictionary
samtools dict reference.fa -o reference.dict
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.
- 3d ago First seen · 377 lines · 32 tokens per session scan A 5f1fd07f7563
bio-reference-operations is a skill published in the GitHub repository GPTomics/bioSkills (1,198 stars, last pushed 18d ago), licensed MIT. It adds 32 tokens to every session and 3,321 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). 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
Perform bounded, local exploratory analysis of explicitly supported scientific files. Use for 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…
mapping-to-snomed
Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED CT, run an ECL…
auditing-subgroup-fairness
Audit an OpenMed NER or de-identification model for performance disparities across demographic subgroups (sex, age band, race/ethnicity when available) using openmed.eval.fairnessreport. Use when the user wants per-subgroup recall and leakage, wants to check whether de-identification under-protects a group, wants to…
overleaf-sync
Two-way sync between a local paper directory and an Overleaf project, so ARIS audit/edit workflows stay on the local copy while collaborators edit in the Overleaf web UI. Use when user says "同步 overleaf", "overleaf sync", "推送到 overleaf", "connect overleaf", "Overleaf 桥接", "pull overleaf", "push overleaf", or wants to…
mixed-precision
Use FP16/BF16 mixed precision to accelerate training and reduce memory. Use when optimizing GPU performance.