bio-batch-downloads - Batch-download large datasets from NCBI
Downloads large NCBI datasets with history-server batching, rate limiting, retries, checkpointing, and integrity validation.
Tags
Updated: 2026-09-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Select retrieval strategies
- Batch NCBI requests
- Use the history server
- Apply request rate limits
- Retry failed downloads
- Checkpoint download progress
- Resume interrupted downloads
- Validate download integrity
- Compare E-utilities and Datasets
Inputs
- NCBI database
- Search query
- NCBI identifier list
- Output file path
- Checkpoint file path
- NCBI email
- NCBI API key
Outputs
- Downloaded sequence files
- Checkpoint files
- Resumable download state
- Validated download data
Requirements
- Python 3 environment
- Biopython 1.83 or later
- NCBI Datasets CLI 16.0 or later
- Entrez Direct 21.0 or later
- NCBI network access
- NCBI API credentials for bulk downloads