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{"id":9753,"date":"2022-10-13T10:08:47","date_gmt":"2022-10-13T14:08:47","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=9753"},"modified":"2022-10-13T10:08:47","modified_gmt":"2022-10-13T14:08:47","slug":"new-pgap-available","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/","title":{"rendered":"New version of PGAP now available!"},"content":{"rendered":"<p>We are happy to announce a new version of the stand-alone <a href=\"https:\/\/github.com\/ncbi\/pgap\/releases\/tag\/2022-10-03.build6384\">Prokaryotic Genome Annotation Pipeline (PGAP)<\/a>. This version helps you interpret your results by providing an estimate of the completeness and contamination of your PGAP-annotated genome assembly using <a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/25977477\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pgap-20221013\">CheckM<\/a>.<\/p>\n<p>CheckM uses the presence of a set of lineage-specific genes for the species provided\u00a0 or the species returned by the taxonomy check (–taxcheck, –auto-correct-tax). The higher the completeness and the lower the contamination, the better the assembly is! If contamination is a concern, please try <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/07\/28\/fcs-beta-tool\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pgap-20221013\">FCS-GX<\/a>, a highly sensitive tool for detecting foreign contaminants in prokaryotic and eukaryotic genome assemblies.<\/p>\n<p>This new release also contains code changes that improve prediction of some long genes, especially in low complexity regions. And, as with every release, PGAP incorporates incremental improvements from expert curators of the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/protfam?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=pgap-20221013\">Protein Family Model<\/a> collection that increase the precision of PGAP\u2019s structural and functional annotation.<\/p>\n<p>Please try this new version and <a href=\"https:\/\/github.com\/ncbi\/pgap\">share your experience<\/a> with us!<\/p>\n<p> <\/p>\n","protected":false},"excerpt":{"rendered":"<p>We are happy to announce a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP). This version helps you interpret your results by providing an estimate of the completeness and contamination of your PGAP-annotated genome assembly using CheckM. CheckM uses the presence of a set of lineage-specific genes for the species provided\u00a0 or the … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">New version of PGAP now available!<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":9797,"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":"New version of PGAP 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":[15779425,693060702],"table_tags":[],"class_list":["post-9753","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-pgap","tag-protein-family-model"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>New version of PGAP 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\/2022\/10\/13\/new-pgap-available\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"New version of PGAP now available! - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"We are happy to announce a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP). This version helps you interpret your results by providing an estimate of the completeness and contamination of your PGAP-annotated genome assembly using CheckM. CheckM uses the presence of a set of lineage-specific genes for the species provided\u00a0 or the … Continue reading New version of PGAP now available! →\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-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=\"2022-10-13T14:08:47+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/10\/PGAP_Blog-1-e1665668789518.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=\"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\/2022\/10\/13\/new-pgap-available\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"New version of PGAP now available!\",\"datePublished\":\"2022-10-13T14:08:47+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/\"},\"wordCount\":165,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/10\/PGAP_Blog-1-e1665668789518.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"NCBI Prokaryotic Genome Annotation Pipeline (PGAP)\",\"Protein Family Model\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/\",\"name\":\"New version of PGAP now available! - NCBI Insights\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/10\/PGAP_Blog-1-e1665668789518.png?fit=1100%2C575&ssl=1\",\"datePublished\":\"2022-10-13T14:08:47+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/10\/13\/new-pgap-available\/#primaryimage\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/10\/PGAP_Blog-1-e1665668789518.png?fit=1100%2C575&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/10\/PGAP_Blog-1-e1665668789518.png?fit=1100%2C575&ssl=1\",\"width\":1100,\"height\":575,\"caption\":\"Image of DNA bases in the background in red, blue and green. 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