Tag: RefSeq

Now Available: Updated Bacterial and Archaeal Reference Genome Collection

Now Available: Updated Bacterial and Archaeal Reference Genome Collection

Download the updated bacterial and archaeal reference genome collection! We built this collection of 23,063 genomes by selecting the “best” genome assembly for each species among the 450,000+ prokaryotic genomes in RefSeq.  

What’s new?  
  • Two species are represented in this collection for the first time  
  • 283 species are represented by a better assembly 
  • Six species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment  

Continue reading “Now Available: Updated Bacterial and Archaeal Reference Genome Collection” →

Now Available: RefSeq Release 233

Now Available: RefSeq Release 233

RefSeq release 233 is now available online and from the FTP site! You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also as divided by logical groupings.   

What’s included in this release? 

As of January 26, 2026, this full release incorporates genomic, transcript, and protein data containing:  

  • 578,285,616 records 
  • 442,943,508 proteins 
  • 76,278,418 RNAs 
  • Sequences from 174,157 organisms 

Continue reading “Now Available: RefSeq Release 233” →

Now Available! NCBI Hidden Markov Models (HMM) Release 19.0

Now Available! NCBI Hidden Markov Models (HMM) Release 19.0

Download release 19.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.  

What’s new?  

Release 19.0 contains:  

  • 18,513 HMMs maintained by NCBI  
  • 465 new HMMs since release 18.0  

Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 19.0” →

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 22,420 genomes by selecting the “best” genome assembly for each species among the 450,000+ prokaryotic genomes in RefSeq. 

What’s new? 
  • One species is represented in this collection for the first time 
  • 323 species are represented by a better assembly
  • Six species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment 

Continue reading “An Updated Bacterial and Archaeal Reference Genome Collection is Available!” →

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

An Updated Bacterial and Archaeal Reference Genome Collection is Available!

Download the updated bacterial and archaeal reference genome collection! We built this collection of 22,082 genomes by selecting the “best” genome assembly for each species among the 440,000+ prokaryotic genomes in RefSeq. 

What’s new? 
  • 28 species are represented in this collection for the first time 
  • 228 species are represented by a better assembly 
  • Six species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment 

Continue reading “An Updated Bacterial and Archaeal Reference Genome Collection is Available!” →

Now Available! NCBI Hidden Markov Models (HMM) Release 18.0

Now Available! NCBI Hidden Markov Models (HMM) Release 18.0

Download release 18.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. 

What’s new? 

Release 18.0 contains: 

  • 18,057 HMMs maintained by NCBI 
  • 631 new HMMs since release 17.0 

Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 18.0” →

Now Available: Updated Bacterial and Archaeal Reference Genome Collection

Now Available: Updated Bacterial and Archaeal Reference Genome Collection

Download the updated bacterial and archaeal reference Genome collection! We built this collection of 21,794 genomes by selecting the “best” genome assembly for each species among the 400,000+ prokaryotic genomes in RefSeq, which is 536 more than was included in the January release. Continue reading “Now Available: Updated Bacterial and Archaeal Reference Genome Collection” →

RefSeq Release 229 is Now Available!

RefSeq Release 229 is Now Available!

Check out RefSeq release 229, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

What’s included in this release?

As of March 3, 2025, this full release incorporates genomic, transcript, and protein data containing:

  • 522,879,448 records
  • 399,577,538 proteins
  • 68,985,910 RNAs
  • Sequences from 164,117 organisms 

Continue reading “RefSeq Release 229 is Now Available!” →

An updated bacterial and archaeal reference genome collection is available!

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. 

Continue reading “An updated bacterial and archaeal reference genome collection is available!” →