{"id":6087,"date":"2015-10-09T16:10:17","date_gmt":"2015-10-09T16:10:17","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/?p=6087"},"modified":"2016-06-16T20:30:27","modified_gmt":"2016-06-16T20:30:27","slug":"confirm-ngs-variants-ashg-2015","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/confirm-ngs-variants-ashg-2015\/","title":{"rendered":"Finally! An Automated Workflow to Confirm Your NGS Variants | ASHG 2015"},"content":{"rendered":"<p>If you work in a clinical research la<img loading=\"lazy\" decoding=\"async\" class=\" wp-image-6091 alignleft\" src=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-Sanger-confirmed.png\" alt=\"NGC Module - Sanger confirmed\" width=\"181\" height=\"181\" srcset=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-Sanger-confirmed.png 186w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-Sanger-confirmed-150x150.png 150w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-Sanger-confirmed-80x80.png 80w\" sizes=\"auto, (max-width: 181px) 100vw, 181px\" \/>b, you might be familiar with the manual process of comparing your data from your <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/brands\/ion-torrent.html?socid=social_btb\" target=\"_blank\">NGS platform<\/a> with data from your <a href=\"https:\/\/www.thermofisher.com\/us\/en\/home\/life-science\/sequencing\/sanger-sequencing\/sanger_sequencing_method.html?socid=social_btb\" target=\"_blank\">Sanger Sequencing<\/a> system. It is a time consuming process that probably requires you to rearrange your calendar depending on the quality of your data. Well, good news! NGS confirmation is a snap with one of the newest software solutions from Applied Biosystems<sup>\u00ae<\/sup>.<\/p>\n<p>At ASHG 2015 in Baltimore, Venkatesh Moktali led two live demo sessions at the Thermo Fisher Scientific booth, giving customers a quick glimpse of how these new software solutions can streamline their NGS confirmation workflow. We managed to catch up with Venkatesh for a few minutes before his demo to talk about what he is bringing to the table.<\/p>\n<p><iframe loading=\"lazy\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/rlYr-9INOS8?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>The new workflow using the <a href=\"https:\/\/www.thermofisher.com\/order\/catalog\/product\/A28221?socid=social_btb\">Next Generation Sequencing Confirmation<\/a> (NGC) module consists of five simple steps:<\/p>\n<ol>\n<li><strong>Import your sanger \u201c.ab1\u201d files<\/strong> from any Capillary \u00a0\u00a0\u00a0electrophoresis instrument<\/li>\n<li><strong>Create a Reference<\/strong> to map the variants and <strong>upload your vcf file<\/strong> containing NGS variants<\/li>\n<li><strong>Organize your data into Amplicons<\/strong> for grouping of reads<\/li>\n<li><strong>Set parameters<\/strong> for Trimming, Filtering and Alignment.<\/li>\n<li><strong>Review<\/strong> your settings and run the analyses.<\/li>\n<\/ol>\n<p><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-6088 aligncenter\" src=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-1.png\" alt=\"NGC Module - chart 1\" width=\"627\" height=\"394\" srcset=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-1.png 711w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-1-300x189.png 300w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-1-400x251.png 400w\" sizes=\"auto, (max-width: 627px) 100vw, 627px\" \/><\/p>\n<p>The NGC module shows the comparison of variants from each of the sequencing platforms through an overview pane that puts the variants into two tracks supported by Sanger reads piled up in another track. The module also lets you review your variants and choose the highly confident and confirmed variants through a review table:<br \/>\n<img loading=\"lazy\" decoding=\"async\" class=\" wp-image-6089 aligncenter\" src=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-2.png\" alt=\"NGC Module - chart 2\" width=\"648\" height=\"221\" srcset=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-2.png 666w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-2-300x102.png 300w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-2-400x136.png 400w\" sizes=\"auto, (max-width: 648px) 100vw, 648px\" \/><\/p>\n<p>Finally, you can view your confirmed variants and total variants in a beautiful Venn diagram that gives you a snapshot of your results. The results can also be downloaded in vcf format that consists of all your review results.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-6090 aligncenter\" src=\"http:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-3.png\" alt=\"NGC Module - chart 3\" width=\"642\" height=\"459\" srcset=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-3.png 807w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-3-300x214.png 300w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-3-768x549.png 768w, https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2015\/10\/NGC-Module-chart-3-400x286.png 400w\" sizes=\"auto, (max-width: 642px) 100vw, 642px\" \/>Looks easy enough? <a href=\"https:\/\/www.thermofisher.com\/uk\/en\/home\/cloud\/all-analysis-modules\/sanger-analysis-modules.html?socid=social_btb\">Give it a try! <\/a>\u00a0The NGC module is now FREE on <a href=\"https:\/\/apps.thermofisher.com\/apps\/dashboard\/#\/apps?socid=social_btb\">Thermo Fisher Cloud<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>If you work in a clinical research lab, you might be familiar with the manual process of comparing your data from your NGS platform with data from your Sanger Sequencing system. It is a time consuming process that probably requires you to rearrange your calendar depending on the quality of your data. Well, good news!<\/p>\n","protected":false},"author":117,"featured_media":6090,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_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":""},"categories":[184,113,108],"tags":[17,31,11,6,25],"division":[],"class_list":{"0":"post-6087","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-bioinformatics","8":"category-events-and-tradeshows","9":"category-lab-tips-and-tricks","10":"tag-applied-biosystems","11":"tag-ashg15","12":"tag-ion-torrent","13":"tag-next-generation-sequencing","14":"tag-sanger-sequencing","15":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.8 (Yoast SEO v27.8) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Finally! 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