ENCODE Toolkit vs Graphiti MCP

A side-by-side comparison of two AI, Data & Knowledge servers — tools, transport, auth, maintenance, and copy-paste config for each.

	ENCODE Toolkit Search ENCODE, cross-reference 14 genomics databases, run analysis pipelines, and generate publication-ready methods from natural language. Unverified stdio (local) No auth Python	Graphiti MCP Temporal knowledge-graph memory for agents: add episodes and search facts over FalkorDB or Neo4j, from Zep. Unverified HTTP (remote) API key Python
Category	AI, Data & Knowledge	AI, Data & Knowledge
Language	Python	Python
Transport	stdio (local)	HTTP (remote)
Auth	None	API key
GitHub stars	35	28k
Last commit	1 month ago	1 month ago
Verified
Actively maintained
Install	`claude mcp add encode -- uvx encode-toolkit`	`git clone https://github.com/getzep/graphiti.git && cd graphiti/mcp_server && docker compose up`
Repo	Open	Open

Verdict

Pick ENCODE Toolkit if you want a local (stdio) server that keeps data on your machine, and you want zero-setup with no API key.

Pick Graphiti MCP if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option.

Add ENCODE Toolkit

Install / run

claude mcp add encode -- uvx encode-toolkit

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "uvx",
      "args": [
        "encode-toolkit"
      ]
    }
  }
}

Requires `uv` (the Python package runner). Install it from https://docs.astral.sh/uv/ if `uvx` is not found.

Add Graphiti MCP

Install / run

git clone https://github.com/getzep/graphiti.git && cd graphiti/mcp_server && docker compose up

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "graphiti-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "http://localhost:8000/mcp/"
      ]
    }
  }
}

Claude Desktop connects to remote servers through the `mcp-remote` proxy (installed on first run via npx). Restart Claude Desktop after saving.

FAQ

ENCODE Toolkit or Graphiti MCP — which is better?

Pick ENCODE Toolkit if you want a local (stdio) server that keeps data on your machine, and you want zero-setup with no API key. Pick Graphiti MCP if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option.

Can I use both ENCODE Toolkit and Graphiti MCP?

Yes — MCP clients let you enable multiple servers at once. Add both configs to your client's mcpServers and use whichever tool fits the task.

Do ENCODE Toolkit and Graphiti MCP work with Claude, Cursor and Windsurf?

Both do. Copy the per-client config below into Claude Desktop, Cursor, or Windsurf.

View ENCODE Toolkit →View Graphiti MCP →More comparisons →