{"id":14373,"date":"2025-01-14T11:40:55","date_gmt":"2025-01-14T16:40:55","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=14373"},"modified":"2025-01-14T11:40:55","modified_gmt":"2025-01-14T16:40:55","slug":"updated-bacterial-and-archaeal-reference-genome-collection-2","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2025\/01\/14\/updated-bacterial-and-archaeal-reference-genome-collection-2\/","title":{"rendered":"An updated bacterial and archaeal reference genome collection is available!"},"content":{"rendered":"

Download the updated bacterial and archaeal reference genome collection<\/a>! 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<\/a>.<\/p>\n

What’s new?<\/h4>\n

As previously announced<\/a>, we updated our release process:<\/p>\n

    \n
  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.<\/span><\/li>\n
  2. There is now a history tracking file<\/a> available under the ASSEMBLY_REPORTS path on FTP<\/a> that lists the history of reference genome selection, including both prokaryotes and eukaryotes.\u00a0<\/span><\/li>\n<\/ol>\n

    <\/p>\n

    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<\/a> (fourth in the menu) as well as the database on the Microbial Nucleotide BLAST page<\/a> with this updated collection. You can also run BLAST searches against the proteins annotated on these reference genomes<\/a> (second in the menu).<\/p>\n

    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<\/a> for details.<\/p>\n

    Stay up to date<\/h5>\n

    Follow us on social\u202f<\/span>@NCBI<\/span><\/a>\u202fand\u202f<\/span>join our mailing list<\/span><\/a>\u202fto keep up to date with our reference genome collection\u202fand other NCBI news.\u202f\u202f<\/span>\u00a0<\/span>\u00a0<\/span><\/p>\n

    We want to hear from you!<\/h5>\n

    If you have questions or would like to provide feedback, please reach out to us at info@ncbi.nlm.nih.gov<\/a>.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"

    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: There is now an incremental process. In addition to quarterly releases, there will … Continue reading An updated bacterial and archaeal reference genome collection is available!<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13954,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"An updated bacterial and archaeal reference genome collection is available!","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[77187,27739816],"table_tags":[],"class_list":["post-14373","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-refseq"],"jetpack_publicize_connections":[],"yoast_head":"\nAn updated bacterial and archaeal reference genome collection is available! - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2025\/01\/14\/updated-bacterial-and-archaeal-reference-genome-collection-2\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"An updated bacterial and archaeal reference genome collection is available! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Download the updated bacterial and archaeal reference genome collection! 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