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Reference Sequence Window: Bases by MD5 Checksum, Start and End (GA4GH refget, ENA)

refget/sequence-bases

Returns the bases of a window of one reference sequence held in the European Nucleotide Archive's CRAM reference registry, selected by the sequence's 32-character MD5 checksum and a 0-based start (inclusive) and end (exclusive). The window can be at most 65,536 bases and end must be greater than start; a window past the end of the sequence is rejected. Check the sequence length first with refget/sequence-metadata. Data from the European Nucleotide Archive (EMBL-EBI), served by Eden Engine; not an official ENA or EMBL-EBI product.

activeper callv1

Price

$0.0026 per call

You pay the price shown. If a call turns out to cost more than its quote, you pay the actual price, capped at twice the quote. No monthly minimum. Top-ups start at $0.50.

Data source

European Nucleotide Archive (EMBL-EBI)

Data from the European Nucleotide Archive (ENA) CRAM reference registry, EMBL-EBI, through its GA4GH refget service. INSDC sequence data carries no use restrictions. Served by Eden Engine; not an official EMBL-EBI product.

Use it

Five steps: search, inspect, learn, run, settle. No per-tool setup; your agent reaches this tool through the meta-tools it already has.

Connect once and your AI can find and run this tool, and any other it needs.

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agent
// 1. search: find the tool
omnial_search({ query: "what you need" })

// 2. inspect: price and input schema
omnial_inspect({ tool: "refget/sequence-bases" })

// 3. learn: read the usage guide at runtime
omnial_learn({ tool: "refget/sequence-bases" })

// 4. run: price the exact call first, then run it
omnial_execute({ tool: "refget/sequence-bases", input: { /* see input_schema */ }, dry_run: true })
omnial_execute({ tool: "refget/sequence-bases", input: { /* ... */ } })

// 5. settle: the call is charged when it finishes, nothing to do

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Pricing

Every charge this tool can incur.

ChargePrice
Per call
$0.0026
Updated
Oct 25, 2026

Input and output schemas

Input schema
input_schema.json
{
  "type": "object",
  "required": [
    "checksum",
    "start",
    "end"
  ],
  "properties": {
    "end": {
      "type": "integer",
      "maximum": 2147483647,
      "minimum": 1,
      "description": "Where to stop, counting from 0 (exclusive). Must be greater than start, at most 65,536 greater, and no more than the sequence length. A wider window fails."
    },
    "start": {
      "type": "integer",
      "maximum": 2147483646,
      "minimum": 0,
      "description": "First base to return, counting from 0 (inclusive)."
    },
    "checksum": {
      "type": "string",
      "pattern": "^[0-9a-f]{32}$",
      "description": "The MD5 checksum of the sequence as 32 lowercase hexadecimal characters, for example 3332ed720ac7eaa9b3655c06f6b9e196 (the phiX174 genome)."
    }
  },
  "additionalProperties": false
}
Output schema
output_schema.json
{
  "type": "object",
  "required": [
    "sequence",
    "length"
  ],
  "properties": {
    "length": {
      "type": "integer",
      "description": "Number of bases returned."
    },
    "sequence": {
      "type": "string",
      "description": "The bases of the window as one string, in the case the registry stores them."
    }
  },
  "description": "The requested window.",
  "additionalProperties": false
}