Check whether the NCBI datasets/dataformat CLI tools are installed and, if not, download and install them automatically. Call this tool once before using any download or format-conversion tools.

Returns the install status, binary paths, and version string.

Search NCBI for genome assemblies matching a taxon name or tax ID.

Returns assembly metadata including accession numbers, organism info, assembly statistics, annotation status, and submission details.

Args: taxon: Taxon name (e.g. "human", "Mus musculus") or NCBI tax ID assembly_level: Filter by level — chromosome, complete_genome, contig, scaffold assembly_source: Filter by source — all, genbank, refseq reference_only: Return only reference/representative genomes annotated_only: Return only annotated genomes limit: Maximum number of assemblies to return (capped by server config)

Retrieve genome assembly metadata for one or more NCBI accessions.

Args: accessions: RefSeq or GenBank assembly accessions (e.g. ["GCF_000001405.40", "GCA_000001405.29"])

Download a genome data package for one or more assembly accessions.

Returns the local path to the downloaded ZIP file.

Args: accessions: RefSeq/GenBank assembly accessions include: Data types — genome, rna, protein, cds, gff3, gbff, seq-report. Defaults to ["genome"]. output_dir: Directory for the download. Uses NCBI_DOWNLOAD_DIR if omitted. dehydrated: Download a lightweight dehydrated package (use rehydrate_genome_package to fetch the actual sequence files).

Download genome data packages for assemblies matching a taxon.

For taxa with many assemblies, use dehydrated=True first, then call rehydrate_genome_package to fetch only the data you need.

Args: taxon: Taxon name or NCBI tax ID include: Data types — genome, rna, protein, cds, gff3, gbff, seq-report output_dir: Directory for the download dehydrated: Download a dehydrated package (recommended for large taxa) reference_only: Download only the reference/representative genome

Fetch the full sequence files for a dehydrated genome package.

Args: package_path: Path to the dehydrated ZIP file or its extracted directory.

Convert a genome JSONL data report from a downloaded package to TSV.

Args: jsonl_path: Path to the genome data_report.jsonl file inside the package. fields: Optional list of fields to include. Omit to use the default set.

Get taxonomy metadata for a taxon — lineage, rank, scientific name, common names, and child taxa.

Args: taxon: Taxon name (e.g. "human", "Bacteria") or NCBI tax ID

Download a taxonomy data package for a given taxon.

Args: taxon: Taxon name or NCBI tax ID output_dir: Directory for the download