Download the updated bacterial and archaeal reference genome collection! We built this collection of 20,403 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). Changes have been made to the selection criteria including upgrades for type and complete assemblies resulting in a much larger set of changes as compared to previous updates.
What’s New?
2,298 species have an updated reference
1,123 species are represented in this collection for the first time
1,125 species have a better reference assembly than in the April 2024 set
50 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment
Effective August 2024, core_nt will become the default
Interested in faster nucleotide BLAST searches with more focused search results? As previously announced, NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it more compact and more efficient. Thanks to your feedback, NCBI’s BLAST is excited to introduce the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size.
Benefits of BLAST core_nt over nt
Enables faster searches
Returns similar top results for most searches
Reduces redundancy for some highly represented organisms
Allows easier download and requires less storage space for database download for standalone BLAST
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
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.
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
NEW in BLAST! We made smaller nucleotide databases to help you find the sequences you need faster and easier. You can now find these databases on the main nucleotide BLAST search page (Figure 1) and even download them (Databases: nt_euk, nt_prok, nt_viruses, nt_others).They are separated by organism type, such as eukaryotes, prokaryotes, viruses, and others (including synthetic sequences).
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
