ENCODE Toolkit vs Memory (Knowledge Graph)

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	Memory (Knowledge Graph) Official MCP server providing persistent, file-backed knowledge-graph memory across sessions. Verified stdio (local) No auth TypeScript
Category	AI, Data & Knowledge	AI, Data & Knowledge
Language	Python	TypeScript
Transport	stdio (local)	stdio (local)
Auth	None	None
GitHub stars	35	74k
Last commit	6 days ago	5 months ago
Verified
Actively maintained
Install	`claude mcp add encode -- uvx encode-toolkit`	`npx -y @modelcontextprotocol/server-memory`
Repo	Open	Open

Verdict

Pick ENCODE Toolkit if you need the broadest set of tools.

Pick Memory (Knowledge Graph) 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 Memory (Knowledge Graph)

Install / run

npx -y @modelcontextprotocol/server-memory

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

{
  "mcpServers": {
    "memory-knowledge-graph": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-memory"
      ],
      "env": {
        "MEMORY_FILE_PATH": "/absolute/path/to/memory.jsonl"
      }
    }
  }
}

FAQ

ENCODE Toolkit or Memory (Knowledge Graph) — which is better?

Pick ENCODE Toolkit if you need the broadest set of tools. Pick Memory (Knowledge Graph) if you want the official, vendor-maintained server, and you prefer the more popular, battle-tested option.

Can I use both ENCODE Toolkit and Memory (Knowledge Graph)?

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 Memory (Knowledge Graph) work with Claude, Cursor and Windsurf?

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

View ENCODE Toolkit →View Memory (Knowledge Graph) →More comparisons →