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{"id":5687,"date":"2021-05-17T13:25:51","date_gmt":"2021-05-17T17:25:51","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=5687"},"modified":"2021-05-17T14:22:42","modified_gmt":"2021-05-17T18:22:42","slug":"vgp-ncbi","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/","title":{"rendered":"Vertebrate Genome Project genome assemblies annotated by NCBI"},"content":{"rendered":"<p>NCBI is an active partner of the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly?LinkName=bioproject_assembly_all&from_uid=489243&utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link1\">Vertebrate Genomes Project (VGP)<\/a>, who recently published a <a href=\"https:\/\/www.nature.com\/articles\/d42859-021-00001-6\">series of papers<\/a> on the initial results of their efforts to sequence all 70,000 vertebrate species.\u00a0 See the VGP <a href=\"https:\/\/www.eurekalert.org\/pub_releases\/2021-04\/ru-tvg042621.php\">press release<\/a>\u00a0 for more details. To date, this project has submitted over <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly?LinkName=bioproject_assembly_all&from_uid=489243\">130 diploid chromosome-level assemblies<\/a> to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link2\">NCBI’s GenBank<\/a>\u00a0 and the <a href=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/home\">European Nucleotide Archive<\/a>.\u00a0 NCBI has annotated 94 of the VGP assemblies from 85 species using the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/annotation_euk\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link3\">NCBI Eukaryotic Genome Annotation Pipeline<\/a>.<\/p>\n<p>These sequence and annotation data are <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly?LinkName=bioproject_assembly_all&from_uid=489243&utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link4\">available<\/a> through NCBI web resources including <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link5\">Gene<\/a>, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/assembly\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link6\">Assembly<\/a>, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/nuccore\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link7\">Nucleotide<\/a>, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protein\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link8\">Protein<\/a>, and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link9\">Datasets<\/a> and are included in the <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/genbank\/\">GenBank<\/a> and <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/refseq\/\">RefSeq<\/a> releases. You can browse the assemblies in the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genome\/gdv?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link10\">Genome Data Viewer<\/a>\u00a0 and <span style=\"font-size: 1.125rem;\">\u00a0download metadata, sequence, and annotation data for the latest assemblies in the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/quickstarts\/command-line-tools\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link12\">VGP BioProject<\/a> using the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/quickstarts\/command-line-tools\/?utm_source=blog&utm_medium=referrer&utm_campaign=refseq-annotation&utm_term=vgp-annot&utm_content=20210517link11\">NCBI Datasets command-line tools<\/a><\/span>\u00a0 as shown below.<!--more--><\/p>\n<p><strong>Downloading VGP data with Datasets<\/strong><\/p>\n<p>The following\u00a0 command-line with the <strong>datasets<\/strong> tool will download a data report with detailed metadata for the latest VGP assemblies:<\/p>\n<div class=\"preformatted panel\">\n<div class=\"preformattedContent panelContent\">\n<pre><strong>datasets download genome accession PRJNA489243 --dehydrated --filename vgp.zip\r\n<\/strong><\/pre>\n<\/div>\n<\/div>\n<p>To retrieve the sequence and annotation data, simply unzip and\u00a0<a class=\"external-link\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/how-tos\/genomes\/large-download\/\" target=\"_blank\" rel=\"nofollow noopener\">rehydrate<\/a>:<\/p>\n<div class=\"preformatted panel\">\n<div class=\"preformattedContent panelContent\">\n<pre><strong>datasets rehydrate --directory vgp_archive<\/strong> \r\n<\/pre>\n<\/div>\n<\/div>\n<p><a href=\"mailto:info@ncbi.nlm.nih.gov?subject=NCBI%20Insights%2020210511%20Request%20Genome%20Annotation\">Contact us<\/a> if you are sequencing your own assemblies and interested in NCBI producing an annotation!<\/p>\n","protected":false},"excerpt":{"rendered":"<p>NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.\u00a0 See the VGP press release\u00a0 for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank\u00a0 and the … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Vertebrate Genome Project genome assemblies annotated by NCBI<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":5702,"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":"Vertebrate Genome Project genome assemblies annotated by NCBI","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":[6595,693060686,574294629,693060707,574293891,3064946,9715],"table_tags":[],"class_list":["post-5687","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-assembly","tag-datasets","tag-eukaryotic-genome-annotation","tag-gdh","tag-genome-data-viewer","tag-nucleotide","tag-protein"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Vertebrate Genome Project genome assemblies annotated by NCBI - 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\/2021\/05\/17\/vgp-ncbi\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Vertebrate Genome Project genome assemblies annotated by NCBI - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.\u00a0 See the VGP press release\u00a0 for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank\u00a0 and the … Continue reading Vertebrate Genome Project genome assemblies annotated by NCBI →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/\" \/>\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=\"2021-05-17T17:25:51+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2021-05-17T18:22:42+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/05\/VGP_Platypus_no_border.png?fit=1133%2C635&ssl=1\" \/>\n\t<meta property=\"og:image:width\" content=\"1133\" \/>\n\t<meta property=\"og:image:height\" content=\"635\" \/>\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=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Vertebrate Genome Project genome assemblies annotated by NCBI\",\"datePublished\":\"2021-05-17T17:25:51+00:00\",\"dateModified\":\"2021-05-17T18:22:42+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/\"},\"wordCount\":194,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2021\/05\/VGP_Platypus_no_border.png?fit=1133%2C635&ssl=1\",\"keywords\":[\"Assembly\",\"Datasets\",\"Eukaryotic genome annotation\",\"GDH\",\"Genome Data Viewer (GDV)\",\"NCBI Nucleotide\",\"Protein\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2021\/05\/17\/vgp-ncbi\/\",\"name\":\"Vertebrate Genome Project genome assemblies annotated by NCBI - 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