What is encode-toolkit?
encode-toolkit is a MCP server by ammawla that search, download, track and analyze functional genomics experiments from the ENCODE Project. It is listed under Other and has 21 GitHub stars.
| Type | Mcp server |
|---|---|
| Author | ammawla |
| Repository | ammawla/encode-toolkit |
| Popularity | 21 GitHub stars |
| Category | Other |
| Security | Low risk (92/100) |
| Rank | #1,278 of 4,418 MCP servers; #214 in Other |
| License | AGPL-3.0 |
| Last commit | 2026-09-27 |
| Runs | Not stated |
| Platforms | Linux |
Is encode-toolkit safe to install?
encode-toolkit scores 92/100 on the MCPMods security check: Low risk. No checks raised a concern. It passed 4 of 6 checks.
MCP server results come from listing signals: who publishes it, where your data goes and what it can do. The code itself is not scanned yet.
| Check | Result |
|---|---|
| Community-built server | Note |
| Where data goes is not stated | Note |
| No credentials mentioned | Pass |
| Read-only by description | Pass |
| No code execution | Pass |
| Source on GitHub | Pass |
How do I install encode-toolkit?
- Find the launch command. The README says how the server starts (npx, uvx, docker or a remote URL) and which API keys it needs.
https://github.com/ammawla/encode-toolkit
- Add it to Claude Code. Replace the part after -- with the command from the README. Remote servers use --transport http with a URL.
claude mcp add encode-toolkit -- <command from README> claude mcp add --transport http encode-toolkit <server-url>
- Check it connected. This lists your MCP servers and their status.
claude mcp list
Or ask Claude to set it up
Paste this into Claude Code and it installs encode-toolkit for you:
Add the "encode-toolkit" MCP server from https://github.com/ammawla/encode-toolkit to Claude Code. Read its README for the launch command and any API keys I need, run claude mcp add, then check that it connects.