Now Available: Updated Bacterial and Archaeal Reference Genome Collection

Download the updated bacterial and archaeal reference Genome collection! We built this collection of 21,794 genomes by selecting the “best” genome assembly for each species among the 400,000+ prokaryotic genomes in RefSeq, which is 536 more than was included in the January release.

What’s new?

1. As previously announced, we now have an incremental release process. You can find a history tracking file available under the ASSEMBLY_REPORTS path on the FTP site that lists the history of reference genome selection, including both prokaryotes and eukaryotes. 
2. You can speed up your BLAST sequence searches by running them against these high-quality genomes instead of all of core_nt or nr. We updated the nucleotide BLAST RefSeq reference genomes database (fourth in the dropdown menu under “Choose Search Set”) as well as the database on the Microbial Nucleotide BLAST page with this updated collection. You can also run BLAST searches against the proteins annotated on these reference genomes (second in the dropdown menu).

The criteria for selecting “the” reference assembly for a given species, within all assemblies available in RefSeq for this species, include assembly contiguity and completeness, and quality of the RefSeq annotation. See the Prokaryotic RefSeq Genomes documentation for details.

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If you have questions or would like to provide feedback, please reach out to us at [email protected].