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{"id":12694,"date":"2024-01-18T12:11:46","date_gmt":"2024-01-18T17:11:46","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=12694"},"modified":"2024-01-18T14:38:24","modified_gmt":"2024-01-18T19:38:24","slug":"updated-bacterial-and-archaeal-reference-genome-collection","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/","title":{"rendered":"Updated Bacterial and Archaeal Reference Genome Collection is Available!"},"content":{"rendered":"<p>Download the updated <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/?taxon=2%2C2157&reference_only=true&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\">bacterial and archaeal reference genome collection<\/a>! 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 <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\">RefSeq<\/a> (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.<\/p>\n<p>The\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/about\/prokaryotes\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118#representative_genomes\">criteria<\/a>\u00a0for selecting the reference assembly for a given species include assembly contiguity and completeness and quality of the RefSeq annotation. <!--more--><\/p>\n<h5>What’s new?<\/h5>\n<ul>\n<li><span style=\"font-size: 17px;\">638 species added to the collection<\/span><\/li>\n<li><span style=\"font-size: 17px;\">283 species represented by a better assembly (compared to the <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/09\/05\/bacterial-archaeal-reference-genomes-collection\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\">August 2023 release<\/a>)<\/span><\/li>\n<li><span style=\"font-size: 17px;\">42 species removed because of changes in NCBI Taxonomy or uncertainty in their species assignment<\/span><\/li>\n<\/ul>\n<p>We updated the\u00a0nucleotide BLAST RefSeq reference genomes database\u00a0(fourth in the Database menu on the\u00a0<a class=\"c-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\" data-sk=\"tooltip_parent\">nucleotide BLAST form<\/a>) as well as the database on the\u00a0<a class=\"c-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\" data-sk=\"tooltip_parent\">Microbial Nucleotide BLAST page<\/a> with this collection. You can also run BLAST searches against the proteins annotated on these reference genomes through the RefSeq Select proteins database (second in the Database menu on the <a class=\"c-link\" href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome&utm_source=ncbi_insights&utm_medium=referral&utm_campaign=prok-rep-genomes-20240118\" data-sk=\"tooltip_parent\">protein BLAST form<\/a>).<\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">Follow us on social\u00a0<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"auto\">@NCBI<\/span><\/a>\u00a0<span data-contrast=\"auto\">and\u00a0<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"auto\">join our mailing list<\/span><\/a>\u00a0<span data-contrast=\"auto\">to keep up to date with the bacterial and archaeal reference genomes collection\u202fand other NCBI news.\u202f\u202f\u202f\u202f<\/span><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335559739":160,"335559740":240}\">Please\u00a0<a class=\"c-link\" href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\" data-sk=\"tooltip_parent\">reach out to us<\/a>\u00a0if you have questions or would like to provide feedback.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>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 … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Updated Bacterial and Archaeal Reference Genome Collection is Available!<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":10443,"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":"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":[77187,34457,53114734,576953096,27739816],"table_tags":[],"class_list":["post-12694","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-taxonomy","tag-blastn","tag-prokaryotic-genome-annotation","tag-refseq"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>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\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"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! 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 … Continue reading Updated Bacterial and Archaeal Reference Genome Collection is Available! →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\" \/>\n<meta property=\"og:site_name\" content=\"NCBI Insights\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/ncbi.nlm\" \/>\n<meta property=\"article:published_time\" content=\"2024-01-18T17:11:46+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-01-18T19:38:24+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1100\" \/>\n\t<meta property=\"og:image:height\" content=\"575\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"NCBI Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@NCBI\" \/>\n<meta name=\"twitter:site\" content=\"@NCBI\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"NCBI Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Updated Bacterial and Archaeal Reference Genome Collection is Available!\",\"datePublished\":\"2024-01-18T17:11:46+00:00\",\"dateModified\":\"2024-01-18T19:38:24+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\"},\"wordCount\":240,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2023\/01\/Prok-2-e1673034929164.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Basic Local Alignment Search Tool (BLAST)\",\"NCBI Taxonomy\",\"Nucleotide BLAST (blastn)\",\"Prokaryotic genome annotation\",\"RefSeq\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/01\/18\/updated-bacterial-and-archaeal-reference-genome-collection\/\",\"name\":\"Updated Bacterial and Archaeal Reference Genome Collection is Available! 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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). 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