{"id":13909,"date":"2024-09-24T09:30:49","date_gmt":"2024-09-24T13:30:49","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=13909"},"modified":"2024-09-24T09:30:49","modified_gmt":"2024-09-24T13:30:49","slug":"public-reports-fcs-tool-results","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/","title":{"rendered":"Access Public Reports of Foreign Contamination Screen (FCS) Tool Results"},"content":{"rendered":"<p><span data-contrast=\"auto\">Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view <\/span><a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/ASSEMBLY_REPORTS\/\"><span data-contrast=\"none\">reports<\/span><\/a><span data-contrast=\"auto\"> generated for all prokaryotic and eukaryotic genomes with NCBI\u2019s quality assurance tool, <\/span><a href=\"https:\/\/github.com\/ncbi\/fcs#readme\"><span data-contrast=\"none\">Foreign Contamination Screen (FCS)<\/span><\/a>,<span data-contrast=\"auto\"> to better understand possible issues that may affect your studies.\u00a0<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">What reports are available?<\/span><\/b><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Summary reports to select better assemblies at thresholds of your choosing.\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Detailed reports to remove or mask contaminant sequences so they don&#8217;t adversely affect analyses. This is particularly useful for building k-mer databases.\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Individual assembly reports available through the FTP link located on <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=fcs-reports-20240924\">NCBI Datasets<\/a> genome pages.<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">Reports are available for all eukaryotic and prokaryotic <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=fcs-reports-20240924\">GenBank<\/a> and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=fcs-reports-20240924\">RefSeq<\/a> assemblies, currently covering over 2.7 million assemblies.\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"5\" data-list-defn-props=\"{&quot;335552541&quot;:1,&quot;335559685&quot;:720,&quot;335559991&quot;:360,&quot;469769226&quot;:&quot;Symbol&quot;,&quot;469769242&quot;:[8226],&quot;469777803&quot;:&quot;left&quot;,&quot;469777804&quot;:&quot;\uf0b7&quot;,&quot;469777815&quot;:&quot;hybridMultilevel&quot;}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\">A <a href=\"https:\/\/ftp.ncbi.nlm.nih.gov\/genomes\/ASSEMBLY_REPORTS\/README_fcs_summary_and_details.txt\">README<\/a> to understand how to interpret and use contamination reports.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<h5><b><span data-contrast=\"auto\">Learn More<\/span><\/b><span data-contrast=\"auto\">\u202f<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">Want to run FCS on your own assembly? For more information about FCS and for step-by-step instructions on how to use it, check out our <\/span><a href=\"https:\/\/github.com\/ncbi\/fcs\/\"><span data-contrast=\"none\">help documentation on GitHub<\/span><\/a><span data-contrast=\"auto\">. <\/span><\/p>\n<p><span data-contrast=\"auto\">Visit the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/docs\/v2\/policies-annotation\/quality\/contamination\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=fcs-reports-20240924\">contamination screening page<\/a> to learn more about the screening process and how assemblies are marked as contaminated.\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\">Read all about FCS in our <\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38409096\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=fcs-reports-20240924\"><span data-contrast=\"none\">recent publication<\/span><\/a><span data-contrast=\"auto\"> in Genome Biology.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">Stay up to date<\/span><\/b><span data-contrast=\"auto\">\u202f<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">FCS is part of the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/datasets\/cgr\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=fcs-reports-20240924\"><span data-contrast=\"none\">NIH Comparative Genomics Resource (CGR)<\/span><\/a><span data-contrast=\"auto\">. CGR facilitates reliable comparative genomics analyses\u202ffor all eukaryotic organisms through an NCBI Toolkit and community collaboration.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_50%22\"><span data-contrast=\"none\">Join our mailing list<\/span><\/a><span data-contrast=\"auto\"> to keep up to date with FCS and other CGR news.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">Questions?<\/span><\/b><span data-contrast=\"auto\">\u202f<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">We want to hear from you! We are making ongoing improvements based on your feedback. If you have questions or would like to provide feedback, please reach out to us at\u202f<\/span><a href=\"mailto:info@ncbi.nlm.nih.gov\"><span data-contrast=\"auto\">info@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"auto\">.<\/span><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335557856&quot;:16777215,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view reports generated for all prokaryotic and eukaryotic genomes with NCBI\u2019s quality assurance tool, Foreign Contamination Screen (FCS), to better understand possible issues that may affect your studies.\u00a0\u00a0 What reports are available?\u00a0 Summary reports to select better assemblies &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Access Public Reports of Foreign Contamination Screen (FCS) Tool Results<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":13911,"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":"Access Public Reports of Foreign Contamination Screen (FCS) Tool Results","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":[693060768,693060858,1201719,693060836,27739816],"table_tags":[],"class_list":["post-13909","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-comparative-genomics-resource-cgr","tag-foreign-contamination-screen-fcs-tool","tag-genbank","tag-ncbi-datasets","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>Access Public Reports of Foreign Contamination Screen (FCS) Tool Results - 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\/24\/public-reports-fcs-tool-results\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Access Public Reports of Foreign Contamination Screen (FCS) Tool Results - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"Do you use genomes from NCBI and are concerned they may contain contaminant sequences? Now you can view reports generated for all prokaryotic and eukaryotic genomes with NCBI\u2019s quality assurance tool, Foreign Contamination Screen (FCS), to better understand possible issues that may affect your studies.\u00a0\u00a0 What reports are available?\u00a0 Summary reports to select better assemblies &hellip; Continue reading Access Public Reports of Foreign Contamination Screen (FCS) Tool Results &rarr;\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\" \/>\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=\"2024-09-24T13:30:49+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/FCS_Reports_Blog-1-e1726149486303.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\/24\/public-reports-fcs-tool-results\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\"},\"author\":{\"name\":\"NCBI Staff\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#\/schema\/person\/4f41ea6a31cea38a9a1b1419c048e50b\"},\"headline\":\"Access Public Reports of Foreign Contamination Screen (FCS) Tool Results\",\"datePublished\":\"2024-09-24T13:30:49+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\"},\"wordCount\":280,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#organization\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/FCS_Reports_Blog-1-e1726149486303.png?fit=1100%2C575&ssl=1\",\"keywords\":[\"Comparative Genomics Resource (CGR)\",\"Foreign Contamination Screen (FCS) Tool\",\"GenBank\",\"NCBI Datasets\",\"RefSeq\"],\"articleSection\":[\"What's New\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\",\"url\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\",\"name\":\"Access Public Reports of Foreign Contamination Screen (FCS) Tool Results - NCBI Insights\",\"isPartOf\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/FCS_Reports_Blog-1-e1726149486303.png?fit=1100%2C575&ssl=1\",\"datePublished\":\"2024-09-24T13:30:49+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/24\/public-reports-fcs-tool-results\/#primaryimage\",\"url\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/FCS_Reports_Blog-1-e1726149486303.png?fit=1100%2C575&ssl=1\",\"contentUrl\":\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/09\/FCS_Reports_Blog-1-e1726149486303.png?fit=1100%2C575&ssl=1\",\"width\":1100,\"height\":575,\"caption\":\"Background lines of ATGC and paper icons. 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