| name | refget-mcp |
| description | Use the Refget MCP (Model Context Protocol) server to search and access reference sequences by hash. Trigger this skill whenever a user wants to search for sequence collections, look up sequences by identifier, verify sequence checksums, browse Refget collections, or integrate sequence access into workflows. Ideal for discovering what sequences are available without local installation. |
Refget MCP Skill
This skill enables you to interact with the Refget MCP server to discover and access reference sequences identified by cryptographic hashes.
What This Skill Does
Refget is a standard GA4GH protocol for accessing reference sequences. The MCP server provides queryable access to sequence collections. Use this when you need to:
- Search available reference sequence collections
- Look up sequence metadata by accession or name
- Verify sequence checksums (MD5, SHA512)
- Discover sequence availability across collections
- Integrate sequence lookup into bioinformatics workflows
When to Use This Skill vs. Refget CLI
- Use Refget MCP when: Searching collections, discovering sequences, checking what's available
- Use Refget CLI when: You need to actually download and query sequences locally
Key Differences from Refgenie
| Aspect | Refgenie | Refget |
|---|
| Purpose | Manages pre-built genome indexes & annotations | Provides access to reference sequences by hash |
| Use Case | Alignment, mapping workflows | Sequence retrieval, validation, distribution |
| Scope | Complete genome builds | Individual sequences across collections |
| Assets | Indexes, alignments, annotations | Sequences, metadata, checksums |
Key Functions Available
refget_collections
List all available reference sequence collections.
Query the MCP with no parameters to discover all sequence collections.
Returns: Collection identifiers, descriptions, and metadata
refget_get_collection
Get detailed information about a specific collection.
Provide:
- collection_id: The collection identifier
Returns: Sequences in collection, metadata, URI endpoints
Usage Patterns
Discovery Pattern
User: "What reference sequences are available?"
→ Use refget_collections to list all collections
→ Present organized by organism/collection type
Collection Search Pattern
User: "Show me sequences in the GRCh38 collection"
→ Use refget_get_collection("GRCh38")
→ List sequences, accessions, and checksums
Sequence Lookup Pattern
User: "What's available for chromosome 22?"
→ Query collections for chr22 entries
→ Return sequence IDs and download URIs
Common Reference Collections
Human
GRCh38 / hg38 - GRC Human Build 38GRCh37 / hg19 - GRC Human Build 37
Mouse
GRCm38 / mm10 - GRC Mouse Build 38GRCm39 / mm39 - GRC Mouse Build 39
Other Organisms
Arabidopsis thaliana - TAIR10Drosophila melanogaster - dm6Danio rerio - GRCz11Saccharomyces cerevisiae - R64
Sequence Access
Get Sequence by Hash
Once you have a sequence hash from a collection, you can retrieve the actual sequence using:
Refget URI format:
https://refget.server/sequence/{hash}?start={start}&end={end}
Parameters:
hash: The sequence hash (MD5 or SHA512)start (optional): Start positionend (optional): End position
Checksum Verification
The MCP returns checksums (MD5, SHA512) for sequence validation
Use to verify downloaded sequences match expected values
Integration Patterns
With Refgenie
User wants full genome build:
→ Use Refgenie for indexes/annotations
→ Use Refget for specific sequences if needed
Sequence Validation
Downloaded a FASTA file?
→ Use Refget MCP to get expected checksums
→ Verify: md5sum file.fa && compare with Refget
Bioinformatics Pipelines
Pipeline needs reference sequences:
→ Query Refget to find collection
→ Get sequence hash/checksum
→ Download if needed via Refget CLI
→ Validate against Refget checksums
Troubleshooting
Collection not found: Try variations of the name (e.g., "GRCh38" vs "hg38")
No sequences in collection: Verify collection exists and is not empty
Need actual sequences: Switch to Refget CLI for downloading
Checksum mismatch: Sequences may have been modified; verify collection version
See Also
