Nextstrain Tools#

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

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

Available Tools#

Nextstrain_get_dataset (Type: NextstrainTool)#

Get metadata and phylogenetic summary for a Nextstrain pathogen dataset. Returns title, update da…

Nextstrain_get_dataset tool specification

Tool Information:

  • Name: Nextstrain_get_dataset

  • Type: NextstrainTool

  • Description: Get metadata and phylogenetic summary for a Nextstrain pathogen dataset. Returns title, update date, sequence count, provenance, maintainers, root attributes, and the complete list of available coloring dimensions with an explicit count. Large datasets such as seasonal H3N2 expose more than 15 colorings.

Parameters:

  • dataset (string) (required) Nextstrain dataset path. Examples: ‘zika’, ‘ebola’, ‘flu/seasonal/h3n2/ha/2y’, ‘dengue/denv1’, ‘mpox/clade-IIb’.

Example Usage:

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

Nextstrain_list_datasets (Type: NextstrainTool)#

List available pathogen phylogenetic datasets from Nextstrain. Returns datasets grouped by pathog…

Nextstrain_list_datasets tool specification

Tool Information:

  • Name: Nextstrain_list_datasets

  • Type: NextstrainTool

  • Description: List available pathogen phylogenetic datasets from Nextstrain. Returns datasets grouped by pathogen (e.g., avian-flu, dengue, ebola, flu, measles, mpox, SARS-CoV-2, zika), each with its true ‘dataset_count’. By default only the first 10 dataset paths per pathogen are listed; when that hides entries the response sets ‘truncated’: true with a ‘truncation_note’, and ‘metadata.total_datasets’ always reports the full catalogue size (not the number listed). Pass datasets_per_pathogen=0 to list every dataset, or page each pathogen group: start with dataset_offset=0 and continue with that group’s next_dataset_offset while has_more is true. Optionally filter by pathogen name. Nextstrain provides real-time molecular epidemiology for public health, tracking how pathogens evolve and spread worldwide.

Parameters:

  • pathogen ([‘string’, ‘null’]) (optional) Optional pathogen name filter. Examples: ‘flu’, ‘ebola’, ‘zika’, ‘dengue’, ‘mpox’. Leave empty for all pathogens.

  • datasets_per_pathogen ([‘integer’, ‘null’]) (optional) Maximum number of dataset paths listed per pathogen (default 10). Set to 0 to list every dataset with no cap, or to a larger number (e.g. 100) to cover the biggest pathogens such as ncov and avian-flu.

  • dataset_limit ([‘integer’, ‘null’]) (optional) Alias for datasets_per_pathogen (page size per pathogen group). Ignored when datasets_per_pathogen is given.

  • dataset_offset (integer) (optional) Zero-based offset applied within every matched pathogen group (default 0). Continue each group using its next_dataset_offset while has_more is true.

Example Usage:

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