{"id":13949,"date":"2024-09-19T11:01:45","date_gmt":"2024-09-19T15:01:45","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13949"},"modified":"2024-09-19T11:01:45","modified_gmt":"2024-09-19T15:01:45","slug":"updated-bacterial-archaeal-reference-genome-collection-available","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/","title":{"rendered":"Updated Bacterial and Archaeal Reference Genome Collection now Available!"},"content":{"rendered":"<p>Download the updated <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/?taxon=2%2C2157&amp;reference_only=true&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919\">bacterial and archaeal reference genome collection<\/a>! We built this collection of 20,403 genomes by selecting the &#8220;best&#8221; genome assembly for each species among the 350,000+ prokaryotic genomes in <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919\">RefSeq<\/a> (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.<\/p>\n<h5>What&#8217;s New?<\/h5>\n<ul>\n<li><span style=\"font-size: 17px;\">2,298 species have an updated reference\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0<\/span><\/li>\n<li><span style=\"font-size: 17px;\">1,123 species are represented in this collection for the first time<\/span><\/li>\n<li><span style=\"font-size: 17px;\">1,125 species have a better reference assembly than in the <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/04\/25\/updated-bacterial-archaeal-reference-genomes-collection\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919\">April 2024 set<\/a><\/span><\/li>\n<li><span style=\"font-size: 17px;\">50 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment\u00a0<\/span><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<p>You can speed up your sequence searches by running them against these high-quality genomes instead of all of NT or NR. We updated the <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919\">Nucleotide BLAST RefSeq reference genomes database<\/a> (fourth in the menu) as well as the database on the <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PAGE_TYPE=BlastSearch&amp;BLAST_SPEC=MicrobialGenomes&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919\">Microbial Nucleotide BLAST page<\/a> with this updated collection. You can also run BLAST searches against the <a href=\"https:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi?PROGRAM=blastp&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919\">proteins annotated on these reference genomes<\/a> (second in the menu).<\/p>\n<p>The criteria for selecting &#8220;the&#8221; 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 <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/about\/prokaryotes\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-ref-genomes-20240919#representative_genomes\">documentation<\/a> for details.<\/p>\n<h5>Stay up to date<\/h5>\n<p><span data-contrast=\"auto\">Follow us on social\u202f<\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"auto\">@NCBI<\/span><\/a><span data-contrast=\"auto\">\u202fand\u202f<\/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><span data-contrast=\"auto\">\u202fto keep up to date with our reference genome collection\u202fand other NCBI news.\u202f\u202f<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n<h5>We want to hear from you!<\/h5>\n<p><span data-contrast=\"auto\">If you have questions or would like to provide feedback, please reach out to us at\u00a0<a href=\"mailto:info@ncbi.nlm.nih.gov\">info@ncbi.nlm.nih.gov<\/a>.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Download the updated bacterial and archaeal reference genome collection! We built this collection of 20,403 genomes by selecting the &#8220;best&#8221; 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 &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Updated Bacterial and Archaeal Reference Genome Collection now Available!<\/span> <span class=\"meta-nav\">&rarr;<\/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":"Updated Bacterial and Archaeal Reference Genome Collection now 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":[77187,693060836,34457,53114734,576953096,27739816],"table_tags":[],"class_list":["post-13949","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-blast","tag-ncbi-datasets","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 now 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\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\" \/>\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 now Available! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Download the updated bacterial and archaeal reference genome collection! We built this collection of 20,403 genomes by selecting the &#8220;best&#8221; 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 &hellip; Continue reading Updated Bacterial and Archaeal Reference Genome Collection now Available! &rarr;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\" \/>\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=\"2024-09-19T15:01:45+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.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\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Updated Bacterial and Archaeal Reference Genome Collection now Available!\",\"datePublished\":\"2024-09-19T15:01:45+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\"},\"wordCount\":281,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Basic Local Alignment Search Tool (BLAST)\",\"NCBI Datasets\",\"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\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/\",\"name\":\"Updated Bacterial and Archaeal Reference Genome Collection now Available! 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We built this collection of 20,403 genomes by selecting the &#8220;best&#8221; 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 &hellip; Continue reading Updated Bacterial and Archaeal Reference Genome Collection now Available! &rarr;","og_url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/","og_site_name":"NCBI Insights","article_publisher":"https:\/\/www.facebook.com\/ncbi.nlm","article_published_time":"2024-09-19T15:01:45+00:00","og_image":[{"width":1100,"height":575,"url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.png","type":"image\/png"}],"author":"NCBI Staff","twitter_card":"summary_large_image","twitter_creator":"@NCBI","twitter_site":"@NCBI","twitter_misc":{"Written by":"NCBI Staff","Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#article","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/"},"author":{"name":"NCBI Staff","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b"},"headline":"Updated Bacterial and Archaeal Reference Genome Collection now Available!","datePublished":"2024-09-19T15:01:45+00:00","mainEntityOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/"},"wordCount":281,"commentCount":0,"publisher":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#primaryimage"},"thumbnailUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.png?fit=1100%2C575&ssl=1","keywords":["Basic Local Alignment Search Tool (BLAST)","NCBI Datasets","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\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#respond"]}]},{"@type":"WebPage","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/","url":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/","name":"Updated Bacterial and Archaeal Reference Genome Collection now Available! - NCBI Insights","isPartOf":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website"},"primaryImageOfPage":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#primaryimage"},"image":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#primaryimage"},"thumbnailUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.png?fit=1100%2C575&ssl=1","datePublished":"2024-09-19T15:01:45+00:00","breadcrumb":{"@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/19\/updated-bacterial-archaeal-reference-genome-collection-available\/#primaryimage","url":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.png?fit=1100%2C575&ssl=1","contentUrl":"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/Prok-5-e1726757192182.png?fit=1100%2C575&ssl=1","width":1100,"height":575,"caption":"Colorful prokaryotic organisms in the background. 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