{"id":66758,"date":"2022-11-30T16:31:44","date_gmt":"2022-11-30T16:31:44","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/?post_type=vf_event&#038;p=66758"},"modified":"2022-11-30T16:31:47","modified_gmt":"2022-11-30T16:31:47","slug":"nan18-01","status":"publish","type":"vf_event","link":"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/events\/nan18-01\/","title":{"rendered":"Using Nanopore Technology for Real Time, Direct, Scalable DNA\/RNA Sequencing"},"content":{"rendered":"\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-53de8397-0f08-449c-b4a4-0fdca47249f2\" data-vf-js-location-nearest-activation-target=\"\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-311a4dae-4712-45c4-bb7c-83f569003b70\" data-vf-js-location-nearest-activation-target=\"\">Speakers<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-88113a31-4a51-4c85-a47e-d124b3842495\" data-vf-js-location-nearest-activation-target=\"\">Programme<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-53de8397-0f08-449c-b4a4-0fdca47249f2\"><h2 class=\"vf-u-sr-only\">Overview<\/h2>\n<h2 class=\"wp-block-heading\">Course Overview<\/h2>\n\n\n\n<p>The goal of this course is to teach the fundamentals of nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. We will start with an introduction into ONT technology and devices, with the goal of covering end to end the workflow for preparation and analysis of bacterial samples using examples of a whole genome approach and a targeted barcoded amplicon approach. This course will cover the wet lab preparation of libraries from genomic DNA, with a focus on the critical steps and potential pitfalls and understanding what constitutes a \u2018good\u2019 sample for purpose of best results using the technology. Also, training includes how to use MinKNOW GUI for GridION and MinION devices and a discussion of the methods available for basecalling and analysis of samples for species identification, including use of opens source tools for mapping and assembly, such as Minimap2 and Canu.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Audience<\/h2>\n\n\n\n<p>This course is directed towards molecular biologists, bioinformaticians, scientists and technicians who want to apply Oxford Nanopore Sequencing technology in their labs. Knowledge of ONT sequencing technology is desirable but not essential.&nbsp;Practical experience with standard molecular biology techniques required.&nbsp;<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Modules\/Resources<\/h2>\n\n\n\n<p>Introduction to ONT devices and latest technology<br>Wet lab training and best practices for sample quality and library preparation for Nanopore sequencing<br>Running MinKNOW and real-time sequencing data handling<br>Introduction to basecalling and analysis tools (ONT and opens source) for analysis of ONT data<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Learning Outcomes<\/h2>\n\n\n\n<p>After this course you should be able to:<br>-Prepare libraries from genomic DNA for amplicon or whole genome approaches to nanopore sequencing<br>-Run ONT devices and assess sequencing performance during a run<br>-Understand the basics of ONT data handling and analysis<br>-Analyse and interpret ONT amplicon data and whole genomic data from bacterial samples<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-311a4dae-4712-45c4-bb7c-83f569003b70\"><h2 class=\"vf-u-sr-only\">Speakers<\/h2>\n<h2 class=\"wp-block-heading\">Speakers, Trainers and Organisers<\/h2>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Coccia_Margherita.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Margherita Coccia            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Oxford Nanopore Technologies Ltd            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                UK            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Micorescu_Michael-1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Michael Micorescu            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Oxford Nanopore Technologies, Ltd            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                UK            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Rudd_Stephen.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Stephen Rudd            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Oxford Nanopore Technologies, Ltd            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                UK            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<h2 class=\"wp-block-heading\">Scientific Organisers<\/h2>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Benes_Vladimir1-2-1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Vladimir Benes            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Coccia_Margherita.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Margherita Coccia            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Oxford Nanopore Technologies Ltd            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                UK            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\">\n<h2 class=\"wp-block-heading\">Course Organisers<\/h2>\n\n\n\n<div class=\"embl-grid\"><div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--block | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"115\" height=\"135\" src=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/Maryann_Smith-1.jpg\" class=\"vf-profile__image\" alt=\"\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" style=\"text-align: center;\">\n                    Maryann Heck            <\/h3>\n    \n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                EMBL Heidelberg            <\/p>\n                <p class=\"vf-profile__text\" style=\"text-align: center;\">\n                Germany            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<\/div>\n<\/div>\n<\/div>\n<\/div><\/div>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-88113a31-4a51-4c85-a47e-d124b3842495\"><h2>Programme<\/h2>\n<p id=\"block-1984fb46-4b9e-4350-bb7b-3decc4627750\"><\/p>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-0a6f9005-6c78-4e0c-9bfb-ce6a00d9e1eb\" href=\"https:\/\/www.embl.org\/about\/info\/course-and-conference-office\/wp-content\/uploads\/EMBL-Course-Using-Nanopore-Technology-for-Real-Time-Direct-Scalable-DNA_RNA-Sequencing-Programme.pdf\">EMBL-Course-Using-Nanopore-Technology-for-Real-Time-Direct-Scalable-DNA_RNA-Sequencing-Programme<\/a><\/div>\n\n\n\n<p><\/p>\n<\/section>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-flow wp-block-group-is-layout-flow\"><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"parent":0,"menu_order":0,"template":"","embl_taxonomy":[],"class_list":["post-66758","vf_event","type-vf_event","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"vf_event_start_date":{"value":"20180612","formatted":"12 June 2018"},"vf_event_end_date":{"value":"20180615","formatted":"15 June 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"},"vf_event_start_time":{"value":"","formatted":""},"vf_event_end_time":{"value":"","formatted":""},"vf_event_location":{"value":["67"],"formatted":["EMBL Heidelberg"]},"vf_event_time_zone":{"value":"europe\/berlin","formatted":"Europe\/Berlin"},"vf_event_ss_subtype":{"value":null,"formatted":null},"vf_event_embo_subtype":{"value":"","formatted":""},"vf_event_featured":{"value":"0","formatted":false},"vf_event_organisers_listing":{"value":"","formatted":""},"vf_event_displayed":{"value":"EMBL Course","formatted":"EMBL 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