Skill Claude CodeCodex
Produce a population diversity and structure report for a Gigwa variant set. Use this when a user asks to summarise genetic diversity, describe population structure, or assess relatedness for a run identified by its variantSetDbId. Walks through dataset-wide MAF/He/Ho/PIC/Fis, principal component analysis (PCA)…
Skill Claude CodeCodex
Get an overview of an entire Gigwa instance and flag anything that needs attention. Use this when a user asks what data is available on a Gigwa server, wants to enumerate databases/projects/runs, or has inherited an instance and needs a health check before analysis. Confirms connectivity, server version and…
Skill Claude CodeCodex
Import a genotype dataset into a Gigwa server and run standard quality control. Use this when a user wants to load a DArTseq SNP/Silico xlsx report or a VCF (.vcf/.vcf.gz) into a Gigwa database, project and run, then verify the import is clean. Covers optional genome-anchoring of DArTseq tag sequences to a reference…
Skill Claude CodeCodex
Run the full quality-control suite on a Gigwa variant set and give a go/no-go verdict for downstream analysis. Use this when a user wants to triage or vet the quality of an already-imported run (identified by its variantSetDbId) before trusting diversity or association results. Runs call rate (worst samples and…
Skill Claude CodeCodex
Characterise the variants and diversity within a single genomic region of a Gigwa variant set. Use this when a user asks about a specific chromosome, contig or coordinate window (e.g. 'chr1' or 'chr1:1000000-2000000') in a run identified by its variantSetDbId. Confirms the contig name, counts variants in the window…
MCP server Claude CodeCodexCursor
MCP server for driving Gigwa installations: import genotype/metadata, run QC and diversity analyses. Runs locally from the gigwa-mcp Python package. Needs 5 environment variables to run.