{"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":"

We are excited to introduce a 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 GenBank<\/a>. If you submit genome assembly data to GenBank, the FCS tool is for you!<\/p>\n

What is the FCS tool?<\/strong><\/p>\n

FCS, a quality assurance process used<\/span><\/span> to make data suitable for submission, consists of two parts: FCS-adaptor<\/a> and 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>\n

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

How do I use FCS?<\/strong><\/p>\n

FCS is available from <\/span><\/span>GitHub<\/span><\/span><\/span><\/a>. Simply download the <\/span>two <\/span>programs (FCS-adaptor and FCS-GX), and follow a few steps as outlined in the Quickstart<\/a>. <\/span>Both tools are also easy and inexpensive to run<\/span>\u00a0on commercial clouds such as Amazon Web Services (AWS) or Google Cloud Platform (GCP), and <\/span>can screen genomes in a fraction of the time of other approaches.<\/span><\/span>\u00a0<\/span><\/p>\n

Why is FCS important?<\/b><\/p>\n

Having high quality data available for analysis is <\/span>necessary<\/span> in order to arrive at accurate conclusions <\/span>during research<\/span>. <\/span>With FCS, r<\/span>apid<\/span> detect<\/span>ion of<\/span> contaminants from foreign organisms in assembled genomes <\/span>ensures <\/span>that <\/span>high value data is being provided for submission and available for reuse. <\/span>We\u2019ve <\/span>already <\/span>used<\/span> FCS-GX <\/span>to <\/span>remove<\/span> over one hundred <\/span>megabases<\/span> of contaminants and thousands of erroneous genes and proteins from previously submitted eukaryote genomes <\/span>to make<\/span> the data more useful for all.<\/span><\/span>\u00a0<\/span><\/p>\n

We want to hear from you!<\/strong><\/p>\n

We will update the FCS tool based on your feedback, so try it out and let us know what you think. Please contact us<\/a> with comments and suggestions.<\/p>\n

FCS is part of the 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

Join our mailing list<\/a> to keep up to date with FCS and other CGR news.<\/p>\n

\n","protected":false},"excerpt":{"rendered":"

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 … Continue reading Foreign Contamination Screen (FCS) tool for GenBank submissions<\/span> →<\/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":"\nForeign 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. 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