Sra Tools#

Configuration File: sra_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the sra_tools.json configuration file.

Available Tools#

SRA_get_experiment (Type: SRATool)#

Get detailed metadata for the first NCBI SRA record matching an accession. Returns the complete r…

SRA_get_experiment tool specification

Tool Information:

  • Name: SRA_get_experiment

  • Type: SRATool

  • Description: Get detailed metadata for the first NCBI SRA record matching an accession. Returns the complete run array present in that record’s eSummary plus runs_returned and runs_complete. For study/sample accessions with multiple experiment records, use SRA_search_experiments to enumerate them rather than assuming this single-record lookup represents the whole study.

Parameters:

  • accession (string) (required) SRA accession number (e.g., ‘SRX26927637’, ‘SRP000001’, ‘SRS000001’)

Example Usage:

query = {
    "name": "SRA_get_experiment",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

SRA_search_experiments (Type: SRATool)#

Search the NCBI Sequence Read Archive (SRA) for sequencing experiments by keyword, organism, stra…

SRA_search_experiments tool specification

Tool Information:

  • Name: SRA_search_experiments

  • Type: SRATool

  • Description: Search the NCBI Sequence Read Archive (SRA) for sequencing experiments by keyword, organism, strategy, or platform. Use the zero-based start offset and next_start while has_more is true to retrieve all matching experiments. Run arrays parsed from each NCBI summary are no longer post-truncated to 10.

Parameters:

  • query (string) (optional) Search keywords (e.g., ‘human gut metagenome’, ‘BRCA1 RNA-Seq’, ‘single cell lung cancer’)

  • organism (string) (optional) Organism name to filter by (e.g., ‘Homo sapiens’, ‘Mus musculus’, ‘human gut metagenome’)

  • library_strategy (string) (optional) Sequencing strategy filter (e.g., ‘RNA-Seq’, ‘WGS’, ‘WXS’, ‘ChIP-Seq’, ‘ATAC-seq’, ‘Bisulfite-Seq’, ‘AMPLICON’)

  • platform (string) (optional) Sequencing platform filter (e.g., ‘ILLUMINA’, ‘PACBIO_SMRT’, ‘OXFORD_NANOPORE’, ‘ION_TORRENT’)

  • limit (integer) (optional) Maximum results to return (1-50, default 10)

  • start (integer) (optional) Zero-based SRA search offset. Continue with next_start while has_more is true.

Example Usage:

query = {
    "name": "SRA_search_experiments",
    "arguments": {
    }
}
result = tu.run(query)