I am trying to start a meta-analysis for which I want to extract some 16S-based information from public databases. Moreover, I want to relate this information with any metadata found in the associated studies (everything from environmental variables to sequencing details).

For this, I realized some databases are available, like NCBI-Nucletotide, NCBI-SRA and EMBL-EBI-ENA, but I am not sure about which one to use or whether I can use them all.

How can I filter only whole 16S sequences? Or even the most used 16S region?

One more thing would be how can I extract all the corresponding metadata?

Has anyone here tried this or anything similar before?

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