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Does any one have a condensed NCBI reference seq database with all the gbff files, which covers mostly all the bacteria and archaea. The current NCBI ReqSeq contains more than 30,000 gbff files. I am looking for a much more curated refseq with less than 30K files in it.

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  • $\begingroup$ Please add more context to this question to explain why you need a reduced refseq dataset. There are lots of different reasons for this, and those reasons will change how the reduction is carried out. $\endgroup$
    – gringer
    Jan 27, 2023 at 19:00

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proGenomes includes a collection of genomes that are representative of different types - https://progenomes.embl.de/download.cgi

Or Genome Updater could be used to filter on unique taxonomy IDs and genome completeness etc.

https://github.com/pirovc/genome_updater

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