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name: specialist-domains description: "Use OmicVerse specialist domains for genetics/post-GWAS, AIRR immune repertoire, molecular structure/drug binding, raw sequencing alignment, amplicon pipelines, and external binary wrappers." disable-model-invocation: true metadata: disco-role: operating license: GPL 3.0

OmicVerse Specialist Domains

Use this sub-skill when the task involves omicverse.genetics, omicverse.airr, omicverse.mol, or omicverse.alignment, especially when the workflow may require optional scientific backends, downloads, or external command-line tools.

For root routing and adjacent domains, return to the OmicVerse root skill. Route core AnnData reading/QC/plotting to core-analysis, table statistics and enrichment to multiomics-statistics, and single-cell biological annotation/trajectory workflows to single-cell-workflows.

Safe Workflow

1. Classify the domain before coding: genetics summary statistics/genotypes, AIRR immune-repertoire AnnData/tables, molecular target/structure/drug binding, or raw sequencing/alignment.
2. Validate inputs before invoking heavy functions. Use scripts/check_specialist_inputs.py for column/schema checks, FASTQ pairing, and target-id sanity checks.
3. Gate side effects. Do not allow downloads, external binary execution, conda installs, or network structure/drug lookups unless the user explicitly approves the operation and output locations.
4. Prefer explicit paths over auto-discovery for command wrappers: pass *_path, simpleaf_bin, alevin_fry_home, genome_dir, db_fasta, and output directories deliberately.
5. Record produced artifacts and assumptions: GWAS canonical column names, allele harmonization decisions, AIRR obs chain fields, FASTQ sample names, genome/index/reference versions, and molecular query source.

Domain Map

User asks for	Use	First checks	Output signal
GWAS QC/association, eQTL, fine-map, coloc, MR, scDRS	ov.genetics	Summary-stat columns, genotype orientation, alleles, sample size, optional backend availability	DataFrames, filtered AnnData, backend result objects, plots
10x V(D)J, AIRR TSV, clonotypes, clonal expansion, repertoire overlap	ov.airr	AnnData.obs AIRR chain slots or contig columns; clone_id before expansion metrics	AIRR AnnData, obs columns, diversity/overlap matrices, plots
SRA to FASTQ/counts, STAR, featureCounts, kb, simpleaf, 16S, DADA2, phylogeny	ov.alignment	FASTQ pair naming, reference/index paths, external binary paths, auto_install policy	Files, matrices, AnnData, command logs
Protein structure, known drugs, pockets, docking	ov.mol	Target ID type, network permission, Python/extras, docking backend availability	MolStructure, pocket/drug DataFrames, docking results, views

Read Next

• Specialist workflows for domain-specific implementation patterns.
• API reference for concrete functions, parameters, and outputs.
• Data formats for GWAS, AIRR, FASTQ, amplicon, and molecular input schemas.
• Troubleshooting for optional extras, external binaries, downloads, allele harmonization, and docking issues.
• Input validator for safe read-only validation before running OmicVerse APIs.