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{"id":8917,"date":"2022-07-28T10:18:29","date_gmt":"2022-07-28T14:18:29","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=8917"},"modified":"2022-07-28T10:18:29","modified_gmt":"2022-07-28T14:18:29","slug":"fcs-beta-tool","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/07\/28\/fcs-beta-tool\/","title":{"rendered":"Foreign Contamination Screen (FCS) tool for GenBank submissions"},"content":{"rendered":"<p>We are excited to introduce a <a href=\"https:\/\/github.com\/ncbi\/fcs#readme\" target=\"_blank\" rel=\"noopener\">Foreign Contamination Screen (FCS) tool<\/a> that you can now run yourself, with enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/genbank\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=fcs-tool-20220728\" target=\"_blank\" rel=\"noopener\">GenBank<\/a>. If you submit genome assembly data to GenBank, the FCS tool is for you!<\/p>\n<p><strong>What is the FCS tool?<\/strong><\/p>\n<p>FCS, a <span class=\"TextRun SCXW168550962 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW168550962 BCX8\" data-ccp-parastyle=\"Normal (Web)\">quality assurance process used<\/span><\/span> to make data suitable for submission, consists of two parts: <a href=\"https:\/\/github.com\/ncbi\/fcs\/wiki\/FCS-adaptor\">FCS-adaptor<\/a> and <a href=\"https:\/\/github.com\/ncbi\/fcs\/wiki\/FCS-GX\">FCS-GX<\/a>. FCS-adaptor searches for short sequences that are used as part of the lab preparation process and sometimes wind up in the final assembly by mistake. FCS-GX searches for sequences from a wide range of organisms including bacteria, fungi, protists, viruses, and others to identify sequences that don’t look like they are from the intended organism. In each case, you receive a report of the coordinates and identities of potential contaminants to be reviewed and removed (see Figure 1 for a sample report of the FCS-GX summary output). Both tools are designed to screen both eukaryote and prokaryote genomes.<\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"9061\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/07\/28\/fcs-beta-tool\/image-2022-07-15-16-49-55-672\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?fit=548%2C308&ssl=1\" data-orig-size=\"548,308\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"image-2022-07-15-16-49-55-672\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?fit=300%2C169&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?fit=548%2C308&ssl=1\" class=\"alignnone size-full wp-image-9061\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?resize=548%2C308&ssl=1\" alt=\"\" width=\"548\" height=\"308\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?w=548&ssl=1 548w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?resize=300%2C169&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?resize=150%2C84&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2022\/07\/image-2022-07-15-16-49-55-672.png?resize=270%2C152&ssl=1 270w\" sizes=\"auto, (max-width: 548px) 100vw, 548px\" \/><\/p>\n<p><em>Figure 1. FCS-GX report showing the summary of contamination identified in a tomato genome. The output indicates there are 83 sequences, adding up to 381 kb total length, to be removed from a mix of insect, fungal, and bacterial sources.<\/em><\/p>\n<p><strong>How do I use FCS?<\/strong><\/p>\n<p><span class=\"TextRun SCXW132548104 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">FCS is available from <\/span><\/span><a class=\"Hyperlink SCXW132548104 BCX8\" href=\"https:\/\/github.com\/ncbi\/fcs\" target=\"_blank\" rel=\"noreferrer noopener\"><span class=\"FieldRange SCXW132548104 BCX8\"><span class=\"TextRun Underlined SCXW132548104 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"none\"><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Hyperlink\">GitHub<\/span><\/span><\/span><\/a><span class=\"TextRun SCXW132548104 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">. Simply download the <\/span><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">two <\/span><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">programs (FCS-adaptor and FCS-GX), and follow a few steps as outlined in the <a href=\"https:\/\/github.com\/ncbi\/fcs\/wiki\/FCS-GX\" target=\"_blank\" rel=\"noopener\">Quickstart<\/a>. <\/span><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">Both tools are also easy and inexpensive to run<\/span><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">\u00a0on commercial clouds such as Amazon Web Services (AWS) or Google Cloud Platform (GCP), and <\/span><span class=\"NormalTextRun SCXW132548104 BCX8\" data-ccp-charstyle=\"Strong\">can screen genomes in a fraction of the time of other approaches.<\/span><\/span><span class=\"EOP SCXW132548104 BCX8\" data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><b>Why is FCS important?<\/b><\/p>\n<p><span class=\"TextRun SCXW46972522 BCX8\" lang=\"EN-US\" xml:lang=\"EN-US\" data-contrast=\"auto\"><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">Having high quality data available for analysis is <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">necessary<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\"> in order to arrive at accurate conclusions <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">during research<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">. <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">With FCS, r<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">apid<\/span> <span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">detect<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">ion of<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\"> contaminants from foreign organisms in assembled genomes <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">ensures <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">that <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">high value data is being provided for submission and available for reuse. <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">We\u2019ve <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">already <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">used<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\"> FCS-GX <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">to <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">remove<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\"> over one hundred <\/span><span class=\"SpellingError SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">megabases<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\"> of contaminants and thousands of erroneous genes and proteins from previously submitted eukaryote genomes <\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\">to make<\/span><span class=\"NormalTextRun SCXW46972522 BCX8\" data-ccp-parastyle=\"Normal (Web)\"> the data more useful for all.<\/span><\/span><span class=\"EOP SCXW46972522 BCX8\" data-ccp-props=\"{"134233117":true,"134233118":true,"201341983":0,"335559740":240}\">\u00a0<\/span><\/p>\n<p><strong>We want to hear from you!<\/strong><\/p>\n<p>We will update the FCS tool based on your feedback, so try it out and let us know what you think. Please <a href=\"mailto:info@ncbi.nlm.nih.gov\">contact us<\/a> with comments and suggestions.<\/p>\n<p>FCS is part of the <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/comparative-genomics-resource\/??utm_source=ncbi_insights&utm_medium=referral&utm_campaign=fcs-tool-20220728\" target=\"_blank\" rel=\"noopener\">NIH Comparative Genomics Resource (CGR)<\/a>, an NLM project to establish an ecosystem to facilitate reliable comparative genomics analyses\u202ffor all eukaryotic organisms.<\/p>\n<p><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_50%22\" target=\"_blank\" rel=\"noopener\">Join our mailing list<\/a> to keep up to date with FCS and other CGR news.<\/p>\n<p class=\"auto-cursor-target\">\n","protected":false},"excerpt":{"rendered":"<p>We are excited to introduce a Foreign Contamination Screen (FCS) tool that you can now run yourself, with enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. If you submit genome assembly data to GenBank, the FCS tool is for you! What is the FCS tool? FCS, a … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2022\/07\/28\/fcs-beta-tool\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Foreign Contamination Screen (FCS) tool for GenBank submissions<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":9015,"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":"Foreign Contamination Screening (FCS) beta tool for GenBank submissions","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":[693060768,1201719,574293892,27739816,579863714],"table_tags":[],"class_list":["post-8917","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-comparative-genomics-resource-cgr","tag-genbank","tag-genome-assemblies","tag-refseq","tag-vecscreen"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Foreign Contamination Screen (FCS) tool for GenBank submissions - 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\/07\/28\/fcs-beta-tool\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Foreign Contamination Screen (FCS) tool for GenBank submissions - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"We are excited to introduce a Foreign Contamination Screen (FCS) tool that you can now run yourself, with enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. If you submit genome assembly data to GenBank, the FCS tool is for you! What is the FCS tool? 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