Genomics MCP

A community-driven Model Context Protocol server that provides unified access to genomic archives, reference databases, and indexed sequencing files. It supports discovery of datasets from EGA, ENA, ENCODE, GEO, and NCBI, as well as transfers of genomic data formats like BAM, CRAM, VCF, and FASTA. The server enables agents to query reference data from HGNC, Ensembl, ClinVar, and gnomAD, facilitating complex genomic analysis workflows directly within AI agent environments.

Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Community listingLocal stdioSource reviewed; not executedPublished by rewire-bio

Vendor documentation

What you can do with it

List sources and search datasets across EGA, ENA, ENCODE, and NCBI
Fetch genomic files like BAM, VCF, or FASTA from remote archives
Query reference databases for gene and variant classifications
Compare genotypes across multiple VCF files in local data folders

Source and maintenance

Community listingRegistry 0.1.0

mcp-registry: io.github.rewire-bio/genomics-mcp@0.1.0 Source repository Project website

Maintenance checked: Oct 31, 2026, 10:27 PM UTC

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

ghcr.io/rewire-bio/genomics-mcp:0.1.0

oci

ghcr.io/rewire-bio/genomics-mcp:0.1.0 package definition

{
  "transport": "stdio",
  "identifier": "ghcr.io/rewire-bio/genomics-mcp:0.1.0",
  "registryType": "oci"
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "genomics-mcp-0-1-0": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "ghcr.io/rewire-bio/genomics-mcp:0.1.0"
      ]
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.

Cline configuration

{
  "mcpServers": {
    "genomics-mcp-0-1-0": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "ghcr.io/rewire-bio/genomics-mcp:0.1.0"
      ]
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.

VS Code configuration

{
  "servers": {
    "genomics-mcp-0-1-0": {
      "type": "stdio",
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "ghcr.io/rewire-bio/genomics-mcp:0.1.0"
      ]
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.

Claude Desktop configuration

{
  "mcpServers": {
    "genomics-mcp-0-1-0": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "--rm",
        "ghcr.io/rewire-bio/genomics-mcp:0.1.0"
      ]
    }
  }
}

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