ENCODE Toolkit vs Genomics MCP
ENCODE Toolkit is an MCP server published by ammawla. Marketplaces we read that list it: 2 (Official MCP Registry, Community GitHub marketplaces). Genomics MCP is an MCP server published by rewire-bio. Marketplaces we read that list it: 1 (Official MCP Registry). As of our marketplace pass on 2026-10-20. This pair was picked by a reader, not by our comparison rule, so search engines are asked not to index the page.
Where each is published
| Marketplace |  ENCODE Toolkit |  Genomics MCP |
|---|---|---|
| Official MCP Registry | Listed Version: 0.3.0-beta.5 Downloads/month (npm): 814 Downloads/week (npm): 37 Forks (GitHub): 5 Stars (GitHub): 21 Not marked · First seen |
Listed Version: 0.1.0 Forks (GitHub): 0 Stars (GitHub): 3 Not marked · First seen |
Each figure is the marketplace's own and is never added up across marketplaces. A marketplace that publishes no figure shows none: no number is not zero.
The facts side by side
| Fact | ENCODE Toolkit | Genomics MCP |
|---|---|---|
| Marketplaces that list it (differs) | 2 (better) | 1 (worse) |
| Stars (GitHub) (differs) | 21 (better) | 3 (worse) |
| Forks (GitHub) (differs) | 5 (better) | 0 (worse) |
| Last release | Not published | Not published |
| Where it runs (differs) | On your machine (encode-toolkit) | On your machine (ghcr.io/rewire-bio/genomics-mcp:0.1.0) |
| Transport | stdio | stdio |
| Tools it declares | Not published | Not published |
| Environment variables it asks for | Not published | Not published |
| Parts of the bundle (differs) | 65 | Not a bundle |
| Licence (differs) | AGPL-3.0-only | Not stated |
| Repository (differs) | github.com/ammawla/encode-toolkit | github.com/rewire-bio/genomics-mcp |
| Changes in the last 7 days | 0 | 0 |
| First seen | 2026-10-11 | 2026-10-11 |
Lines where the two differ have a tinted background and bold values. Where the data itself says which value is better (more marketplaces, a larger figure of the same marketplace, a fresher release, a verified mark on a marketplace that lists both), the better one is also marked green with ▲ and the worse one red with ▼. Where it runs, the transport, the tools, the settings, hooks, the bundle's parts, the licence and the week's changes are marked only as different: more or fewer is not better in itself.
What each says it does
ENCODE Toolkit
20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines
Genomics MCP
Bounded genomic data from archives and indexed files, with versioned reference evidence.
How to run each
ENCODE Toolkit As a local MCP server: npm package
claude mcp add --transport stdio encode-toolkit -- npx -y encode-toolkitGenomics MCP As a local MCP server: Docker image
claude mcp add --transport stdio genomics-mcp -- docker run -i --rm ghcr.io/rewire-bio/genomics-mcp:0.1.0Commands built only from what the marketplaces declare; the full set for every client is on each card.
Tools each declares
Neither one's marketplaces publish a list of tools, so there is nothing to compare.
Settings each asks for
Neither one's marketplaces publish the settings it asks for.
What it can do: ENCODE Toolkit · What it can do: Genomics MCP · Compare two other plugins
Data comes from the Official MCP Registry (registry.modelcontextprotocol.io), CC0 1.0. Data comes from public marketplace files in GitHub repositories of their authors. Figures come from our own regular passes over the marketplaces, last read on . We publish no contact details for plugin publishers.