{"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&amp;reference_only=true&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;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 &#8220;best&#8221; 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&amp;utm_medium=referral&amp;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&amp;utm_medium=referral&amp;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&#8217;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&amp;utm_medium=referral&amp;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&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20240118\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"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-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&amp;BLAST_SPEC=MicrobialGenomes&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;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&amp;BLAST_SPEC=MicrobialGenomes&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;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&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome&amp;utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=prok-rep-genomes-20240118\" target=\"_blank\" rel=\"noopener noreferrer\" data-stringify-link=\"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-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=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5>Questions?<\/h5>\n<p><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;: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 &#8220;best&#8221; 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 &hellip; <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\">&rarr;<\/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 &#8220;best&#8221; 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 &hellip; Continue reading Updated Bacterial and Archaeal Reference Genome Collection is Available! &rarr;\" \/>\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 &#8220;best&#8221; 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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