Download the updated bacterial and archaeal reference genome collection! We built this collection of 19,328 genomes by selecting the “best” genome assembly for each species among the 350,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference).
What’s New?
- 413 species are represented in this collection for the first time
- 198 species are represented by a better assembly
- 27 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment
You can speed up your sequence searches by running them against these high-quality genomes instead of all of NT or NR. We updated the Nucleotide BLAST RefSeq reference genomes database (fourth 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 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.
Stay up to date
Follow us on social @NCBI and join our mailing list to keep up to date with our reference genome collection and other NCBI news.
We want to hear from you!
If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov.