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 

Continue reading “Now Available! Updated Bacterial and Archaeal Reference Genomes Collection” →

Download the updated bacterial and archaeal reference genome collection! This collection (18,941 genomes as of Jan 18, 2024) was built by selecting the “best” genome assembly for each species among the 330,000+ prokaryotic genomes in RefSeq (except for E. coli for which two assemblies were selected as reference). You can speed up your sequence searches by running them against these high-quality genomes instead of the entire nucleotide or protein database.

The criteria for selecting the reference assembly for a given species include assembly contiguity and completeness and quality of the RefSeq annotation. Continue reading “Updated Bacterial and Archaeal Reference Genome Collection is Available!” →

An updated bacterial and archaeal reference genome collection is available! This collection of 18,343 genomes was built by selecting exactly one genome assembly for each species among the 312,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.

The criteria for selecting the reference assembly for a given species include assembly contiguity and completeness and quality of the RefSeq annotation. 

What’s new?

• 790 species were added to the collection
• 199 species are represented by a better assembly (compared to the April 2023 release)
• 70 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment 

Continue reading “Now Available! Updated Bacterial and Archaeal Reference Genomes Collection” →

As previously announced, we are continuously curating a better Prokaryotic Reference Genomes Collection. An updated bacterial and archaeal reference genome collection is now available! This collection of 17,623 genomes was built by selecting exactly one genome assembly for each species among the 283,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference. 

What’s new?

• 480 species were added to this collection 
• 178 species are represented by a better assembly 
• 17 species were removed due to changes in NCBI Taxonomy or uncertainty in their species assignment 

Continue reading “New Release! Updated Bacterial and Archaeal Reference Genomes Collection Now Available” →

An updated bacterial and archaeal reference genome collection is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.

A total of 497 species are included in this collection for the first time. In addition, comparing to the October 2022 set, 174 species are represented by a better assembly and 15 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment. The criteria for selecting one assembly for a given species from all assemblies available in RefSeq for the species include assembly contiguity and completeness and quality of the RefSeq annotation. See the documentation for details.

We have updated the nucleotide BLAST RefSeq reference genomes database (fourth in the menu) as well as the database on the Microbial Nucleotide BLAST page to reflect these changes. You can also run BLAST searches against the proteins annotated on these reference genomes (RefSeq Select proteins database, second in the menu).

An updated bacterial and archaeal representative genomes collection is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to represent their respective species. For the first time, more complete assemblies (as calculated by CheckM) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies here. Continue reading “Now available: Updated prokaryote representative genomes collection” →

An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). See more info here.