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ncbi-datasets-cli

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Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.

When to use

• **Discover**: `datasets download genome taxon human --reference --dehydrated --filename human.zip` (fast; ~MB).
• **Inspect**: `unzip -p human.zip ncbi_dataset/fetch.txt` -- a TSV of all URLs to pull.
• **Pull**: either `datasets rehydrate --directory ./human/` or use `aria2c --input-file=fetch.txt` for parallel pull.

When not to use

• PubMed queries
• SRA reads
• custom Entrez queries
• BLAST searches
• pre-computed alignments (Compara)
• richer protein annotation (UniProt)

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