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List of Publicly Available Datasets
There are many ways to access NCBI. One of the most versatile is the set of Entrez Direct Command Line Utilities, though the syntax can take a little work to learn. Careful though, if you are making many requests in a row NCBI might lock you out and some requests will fail (generally more than 3 requests per second, though you can request more from them).
- RefSeq Prokaryotic Genomes
- Entrez Direct Command Line Utilities
- Batch Entrez
- RefSeq Genomes FTP Site
- Rentrez Package
IMG is especially rich in metadata (including some trait data) - though large batch downloads can be tricky depending on how you want to query the database.
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