Ncbi Sra Tools#

Configuration File: ncbi_sra_tools.json Tool Type: Local Tools Count: 5

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

Available Tools#

NCBI_SRA_get_download_urls (Type: NCBISRATool)#

Get FTP and cloud storage URLs for downloading FASTQ sequencing data from SRA runs. Returns multi…

NCBI_SRA_get_download_urls tool specification

Tool Information:

  • Name: NCBI_SRA_get_download_urls

  • Type: NCBISRATool

  • Description: Get FTP and cloud storage URLs for downloading FASTQ sequencing data from SRA runs. Returns multiple access methods: NCBI FTP URLs for direct .sra file download, AWS S3 URLs for cloud-based access (faster for large-scale analysis), and NCBI web URLs for browser access. Note: Downloaded .sra files require SRA Toolkit (fastq-dump or fasterq-dump) to convert to standard FASTQ format. Essential for programmatic access to petabytes of public sequencing data. Works with SRR (NCBI), ERR (ENA), and DRR (DDBJ) accessions.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: get_download_urls)

  • accessions (unknown) (required) SRA run accession(s) (e.g., ‘SRR000001’, ‘ERR000001’, ‘DRR000001’). Can be single accession or array of accessions.

Example Usage:

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

NCBI_SRA_get_run_info (Type: NCBISRATool)#

Get detailed metadata for SRA run accessions including sequencing platform (ILLUMINA, Oxford Nano…

NCBI_SRA_get_run_info tool specification

Tool Information:

  • Name: NCBI_SRA_get_run_info

  • Type: NCBISRATool

  • Description: Get detailed metadata for SRA run accessions including sequencing platform (ILLUMINA, Oxford Nanopore), instrument model, library strategy (RNA-Seq, WGS), library source (genomic, transcriptomic), library layout (paired/single), sample information, study details, organism, and data statistics (total spots, bases). Essential for understanding experimental design and data characteristics before downloading large FASTQ files. Use SRA run accessions (SRR000001, ERR000001, DRR000001) from NCBI_SRA_search_runs or known accessions.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: get_run_info)

  • accessions (unknown) (required) SRA run accession(s) (e.g., ‘SRR000001’, ‘ERR000001’, ‘DRR000001’). Can be single accession or array of accessions. Use SRR for NCBI, ERR for ENA, DRR for DDBJ.

Example Usage:

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

NCBI_SRA_locate_run_files (Type: NCBISRATool)#

Resolve the current, verified cloud download location(s) plus authoritative file size and md5 che…

NCBI_SRA_locate_run_files tool specification

Tool Information:

  • Name: NCBI_SRA_locate_run_files

  • Type: NCBISRATool

  • Description: Resolve the current, verified cloud download location(s) plus authoritative file size and md5 checksum for an SRA run via the NCBI SRA Data Locator (SDL) service. Unlike NCBI_SRA_get_download_urls (which builds a guessed legacy ftp-trace ByRun path that now returns HTTP 404, and an S3 path with no size/md5/region), this returns the real object: https S3/GCP link, exact byte size, md5, storage region, and modification date. Use SRR/ERR/DRR run accessions. Example: SRR390728 returns size=195174182, md5=29a6a1a0dd0702f45225f2eb93c958b5, location s3:us-east-1 https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR390728/SRR390728. Keyless; no NCBI API key required.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: locate_run_files)

  • accessions (unknown) (required) SRA run accession(s) (e.g., ‘SRR390728’, ‘ERR000001’, ‘DRR000001’). Single accession or array. Use SRR for NCBI, ERR for ENA, DRR for DDBJ.

Example Usage:

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

NCBI_SRA_search_runs (Type: NCBISRATool)#

Search NCBI Sequence Read Archive (SRA) with exact offset pagination by study, organism, sequenci…

NCBI_SRA_search_runs tool specification

Tool Information:

  • Name: NCBI_SRA_search_runs

  • Type: NCBISRATool

  • Description: Search NCBI Sequence Read Archive (SRA) with exact offset pagination by study, organism, sequencing strategy, platform, library source, or free-form query. The response reports the exact count, returned, has_more, and next_offset; continue with offset=next_offset until has_more is false. Returned SRA UIDs can be passed to the metadata and file-location tools.

Parameters:

  • operation (unknown) (optional) Operation type (fixed: search)

  • study (string) (optional) Study accession to search (e.g., ‘SRP000001’, ‘ERP000001’, ‘DRP000001’). Searches in [Study] field.

  • organism (string) (optional) Organism name to filter (e.g., ‘Homo sapiens’, ‘Mus musculus’, ‘SARS-CoV-2’). Searches in [Organism] field.

  • strategy (string) (optional) 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)

  • platform (string) (optional) Sequencing platform to filter. Common values: ‘ILLUMINA’, ‘OXFORD_NANOPORE’, ‘PACBIO_SMRT’, ‘ION_TORRENT’, ‘BGISEQ’

  • source (string) (optional) Library source to filter. Common values: ‘GENOMIC’ (DNA), ‘TRANSCRIPTOMIC’ (RNA), ‘METAGENOMIC’, ‘METATRANSCRIPTOMIC’, ‘SYNTHETIC’, ‘VIRAL_RNA’

  • query (string) (optional) Free-form search query if not using structured filters. Use NCBI query syntax (e.g., ‘(Homo sapiens[Organism]) AND (RNA-Seq[Strategy])’)

  • limit (integer) (optional) Page size (1-100).

  • offset (integer) (optional) Zero-based result offset, mapped to NCBI ESearch retstart. Continue with data.next_offset.

  • sort (string) (optional) Result order. SRA’s esearch supports relevance ordering only (default).

Example Usage:

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