An updated bacterial and archaeal reference genome collection is available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 21,258 genomes by selecting the “best” genome assembly for each species among the 400,000+ prokaryotic genomes in RefSeq.

What’s new?

As previously announced, we updated our release process:

1. There is now an incremental process. In addition to quarterly releases, there will be weekly updates to create references for new species which do not have a reference genome and to correct any inconsistencies in the set of references due to taxonomic merges. As a result, there may be more frequent updates to the reference set.
2. There is now a history tracking file available under the ASSEMBLY_REPORTS path on FTP that lists the history of reference genome selection, including both prokaryotes and eukaryotes. 

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 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.

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We want to hear from you!

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