MCP server for driving Gigwa installations: import genotype/metadata, run QC and diversity analyses.
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<p align="center"> <img src="docs/img/logo.png" alt="Gigwa MCP" width="460"> </p> [](https://glama.ai/mcp/servers/gkanogiannis/gigwa-mcp) [](https://lobehub.com/mcp/gkanogiannis-gigwa-mcp) # Gigwa MCP Server An [MCP](https://modelcontextprotocol.io) server that drives a local or remote [Gigwa](https://github.com/SouthGreenPlatform/Gigwa2) installation over its REST API. It lets an MCP client (Codex CLI / Claude Desktop / Claude Code) run the whole genotyping workflow in plain language: **connect → import genotype data & metadata → run QC and diversity analyses → audit databases for import artifacts**. Built for genomic-resources teams and genebanks, but works with any Gigwa instance. - **Import** DArTseq SNP/Silico xlsx reports (with correct 2-row genotype calling) or plain VCF, plus per-individual metadata. - **Analyse** read-only: genotypes are pulled out of Gigwa and all statistics are computed in Python (scikit-allel / numpy / scipy). Nothing is written back. - **Audit** an existing instance to find databases that were imported badly. - Every analysis returns a chat summary and writes full tables as CSV under `./gigwa_results/<database>/`. ## Table of contents - [Gigwa MCP Server](#gigwa-mcp-server) - [Table of contents](#table-of-contents) - [Overview](#overview) - [Features](#features) - [How it works](#how-it-works) - [Requirements](#requirements) - [Installation](#installation) - [Try it first (no install)](#try-it-first-no-install) - [1. Get it](#1-get-it) - [2. Point your client at it](#2-point-your-client-at-it) - [Installing from the MCPB bundle](#installing-from-the-mcpb-bundle) - [Run with Docker](#run-with-docker) - [Configuration](#configuration) - [Quick start](#quick-start) - [Tool reference](#tool-reference) - [Prompts \& resources](#promp…
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