Cortexa research tool·genomics·ncbi_sra

NCBI SRA Search Runs

Search NCBI Sequence Read Archive (SRA) for NGS/RNA-seq sequencing runs by study accession, organism, sequencing strategy (RNA-Seq, WGS, ChIP-Seq), platform (ILLUMINA, OXFORD_NANOPORE), or library source. Returns SRA UIDs which can be used with other SRA tools to retrieve metadata and download links. Essential for discovering high-throughput sequencing data from public repositories. Use this to find relevant sequencing experiments before accessing the actual FASTQ data files.

Livelast probed 2026-04-30 23:07Z· 117msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 117ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "limit": {
      "default": 20,
      "description": "Maximum number of results to return (default: 20, max: 100)",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "operation": {
      "const": "search",
      "description": "Operation type (fixed: search)"
    },
    "organism": {
      "description": "Organism name to filter (e.g., 'Homo sapiens', 'Mus musculus', 'SARS-CoV-2'). Searches in [Organism] field.",
      "type": "string"
    },
    "platform": {
      "description": "Sequencing platform to filter. Common values: 'ILLUMINA', 'OXFORD_NANOPORE', 'PACBIO_SMRT', 'ION_TORRENT', 'BGISEQ'",
      "type": "string"
    },
    "query": {
      "description": "Free-form search query if not using structured filters. Use NCBI query syntax (e.g., '(Homo sapiens[Organism]) AND (RNA-Seq[Strategy])')",
      "type": "string"
    },
    "sort": {
      "default": "relevance",
      "description": "Sort order for results (default: relevance)",
      "enum": [
        "relevance",
        "pub_date"
      ],
      "type": "string"
    },
    "source": {
      "description": "Library source to filter. Common values: 'GENOMIC' (DNA), 'TRANSCRIPTOMIC' (RNA), 'METAGENOMIC', 'METATRANSCRIPTOMIC', 'SYNTHETIC', 'VIRAL_RNA'",
      "type": "string"
    },
    "strategy": {
      "description": "Sequencing strategy to filter. Common values: 'RNA-Seq' (transcriptomics), 'WGS' (whole genome), 'WXS' (exome), 'ChIP-Seq' (chromatin), 'ATAC-Seq' (accessibility), 'Bisulfite-Seq' (methylation), 'AMPLICON' (targeted), 'Hi-C' (3D genome)",
      "type": "string"
    },
    "study": {
      "description": "Study accession to search (e.g., 'SRP000001', 'ERP000001', 'DRP000001'). Searches in [Study] field.",
      "type": "string"
    }
  },
  "required": [],
  "type": "object"
}

Examples (1)

Default NCBI SRA Search Runs call

public-safeinput

{
  "limit": 3,
  "query": "BRCA1"
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_NCBI_SRA_search_runs
Tool name: NCBI_SRA_search_runs
Added: 2026-04-30 22:47Z
Tags: tooluniverse

NCBI SRA Search Runs

Livelast probed 2026-04-30 23:07Z· 117msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "limit": { "default": 20, "description": "Maximum number of results to return (default: 20, max: 100)", "maximum": 100, "minimum": 1, "type": "integer" }, "operation": { "const": "search", "description": "Operation type (fixed: search)" }, "organism": { "description": "Organism name to filter (e.g., 'Homo sapiens', 'Mus musculus', 'SARS-CoV-2'). Searches in [Organism] field.", "type": "string" }, "platform": { "description": "Sequencing platform to filter. Common values: 'ILLUMINA', 'OXFORD_NANOPORE', 'PACBIO_SMRT', 'ION_TORRENT', 'BGISEQ'", "type": "string" }, "query": { "description": "Free-form search query if not using structured filters. Use NCBI query syntax (e.g., '(Homo sapiens[Organism]) AND (RNA-Seq[Strategy])')", "type": "string" }, "sort": { "default": "relevance", "description": "Sort order for results (default: relevance)", "enum": [ "relevance", "pub_date" ], "type": "string" }, "source": { "description": "Library source to filter. Common values: 'GENOMIC' (DNA), 'TRANSCRIPTOMIC' (RNA), 'METAGENOMIC', 'METATRANSCRIPTOMIC', 'SYNTHETIC', 'VIRAL_RNA'", "type": "string" }, "strategy": { "description": "Sequencing strategy to filter. Common values: 'RNA-Seq' (transcriptomics), 'WGS' (whole genome), 'WXS' (exome), 'ChIP-Seq' (chromatin), 'ATAC-Seq' (accessibility), 'Bisulfite-Seq' (methylation), 'AMPLICON' (targeted), 'Hi-C' (3D genome)", "type": "string" }, "study": { "description": "Study accession to search (e.g., 'SRP000001', 'ERP000001', 'DRP000001'). Searches in [Study] field.", "type": "string" } }, "required": [], "type": "object" }