Download the updated bacterial and archaeal reference genome collection! We built this collection of 23,519 genomes by selecting the “best” genome assembly for each species among the 500,000+ prokaryotic genomes in RefSeq.  

• Twenty-one species are represented in this collection for the first time  
• 114 species are represented by a better assembly 
• Eight species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment  

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 option in the menu) 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 option in the 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 documentation for details.  

Please reach out to us if you have questions or would like to provide feedback.