# Ammawla Encode Toolkit MCP server

Source: https://glimind.com/server/mcp-registry%2Fio.github.ammawla%2Fencode-toolkit
Registry id: `mcp-registry/io.github.ammawla/encode-toolkit`
Status: unknown

## Install

```json
{
  "mcpServers": {
    "ammawla-encode-toolkit-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}
```

Claude Code:

```sh
claude mcp add ammawla-encode-toolkit-mcp-server -- npx -y encode-toolkit
```

## Tools (20)

- `encode_batch_download`: Batch download files by filters.
- `encode_compare_experiments`: Compare two ENCODE experiments.
- `encode_download_files`: Download specific files from ENCODE.
- `encode_export_data`: Export experiment data to CSV/TSV/JSON.
- `encode_get_citations`: Get citations for experiments.
- `encode_get_experiment`: Get details of a specific ENCODE experiment.
- `encode_get_facets`: Get facet counts for ENCODE experiments.
- `encode_get_file_info`: Get detailed info for a specific file.
- `encode_get_metadata`: Get metadata options for ENCODE fields.
- `encode_get_provenance`: Get provenance for a file or accession.
- `encode_get_references`: Get references linked to experiments.
- `encode_link_reference`: Link an experiment to an external reference.
- `encode_list_files`: List files for an experiment with filters.
- `encode_list_tracked`: List tracked experiments with filters.
- `encode_log_derived_file`: Log a derived file with provenance.
- `encode_manage_credentials`: Manage ENCODE access credentials.
- `encode_search_experiments`: Search ENCODE experiments with multiple filters.
- `encode_search_files`: Search files across ENCODE with filters.
- `encode_summarize_collection`: Summarize a collection of experiments.
- `encode_track_experiment`: Track an experiment with publications and pipelines.

Measured by Glimind (https://glimind.com): MCP handshake + tool list only, no tool is ever called. CC BY 4.0.