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batch-downloads

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Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.

When to use

• bulk-fetching tens of thousands of sequences
• pulling all results of a large ESearch
• designing reproducible pipelines
• comparing E-utilities to NCBI Datasets v2 CLI
• implementing checksum-validated downloads
• downloading whole genome assemblies
• downloading all RefSeq for a species
• downloading all gene records for a list

When not to use

• raw sequencing reads
• PubMed metadata only
• ESummary metadata only
• custom queries not in Datasets API

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