Library preparation: Comparing RNA kits
Presenting the range of library preparation kits for RNA sequencing to help choose which kit is more appropriate for certain applications.
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EPI2ME Introduction
Overview of EPI2ME software and workflows
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MinKNOW: Introduction
Introduction to MinKNOW software: key features and IT requirements.
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Priming and loading your flow cell
Flow cell priming and sample loading demonstration.
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Knowledge Exchange: GridION Mk1: delivering ultimate flexibility in the lab
This Knowledge Exchange introduces the GridION Mk1 sequencing device - capable of running up to 5 individually addressable MinION or Flongle Flow Cells.
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A practical demonstration of priming and loading a Flongle flow cell
A short video describing how to prime and load a flongle flow cell.
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A practical demonstration of how to prime and load a PromethION flow cell
In this video you will learn how to prime and load a promethION flow cell
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Flow cell introduction
Introduction to the MinION and GridION flow cells.
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DNA (Lambda) Control Experiment Overview
Overview of Lambda Control Experiment for rapid and ligation sequencing kit.
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EPI2ME Labs Nextflow Workflows demonstration
This video demonstrates running an EPI2ME Labs Nextflow workflow on the command line.
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EPI2ME Labs: wf-human-variation Platform Demo
Practical demonstration on how to launch the "wf-human-variation" workflow using EPI2ME Labs Graphics User Interface.
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Methylation Detection: Sample to Answer Workflow Overview
This video introduces methylation detection capabilities of Nanopore sequencing and includes general recommendations for preparing your library for methylation detection.
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MinKNOW Configuration for Kit 14
Illustration on how to setup a Kit V14 sequencing run using MinKNOW software.
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Kit V14 performance
An overview of Kit 14 performance when compared to previous chemistries.
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Kit V14 introduction and overview
An introduction to Kit 14 and chemistry overview.
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Methylation Detection On MinKNOW
This video describes tools and approaches for methylation detection, setting up a run on the MinKNOW software and tools for downstream analysis of methylation data.
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MinKNOW: Hardware check
Unboxing the MinION device and live demonstration of running hardware check using MinKNOW.
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Introduction to metagenomic assembly
This video introduces concepts, tools, and techniques you can use to assemble genomes using Oxford Nanopore long read metagenomic data.
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Bioinformatics file formats: reference and annotation files
This video will introduce bioinformatics file formats used to store reference sequence and annotated features data, and databases hosting these files
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Introduction to read alignment/mapping
In this video you will learn about read alignment/mapping approaches, file formats and workflows
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Introduction to variant annotation and phasing
In this video you will learn about tools and key terms involved in phasing genetic variation. Tools for the functional annotation of identified variants are also highlighted
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EPI2ME Labs Workflows set up and configuration
This video contains an introduction to using EPI2ME Labs workflows in the command line including commands for installing, updating and running analysis workflows. Increasing the CPU and RAM usage is also described
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Introduction to EPI2ME Labs workflows
This video introduces bioinformatics workflows and nextflow workflows provided through the EPI2ME Labs workflows analysis platform
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Introduction to SNP and indel detection
This video will introduce the general workflow for detection SNP and indel variation, relevant file formats and ONT analysis solutions for detection of SNPs and indels in your data
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Differential gene expression analysis workflows
This video will introduce steps involved required to detect differentially expressed genes and bioinformatics solutions available to help with this process
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Introduction to differential gene expression
This video will introduce an overview of the process for detection of differentially expressed genes and considerations for processing and interpreting transcriptomic data and results
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Introduction to methylation detection
This video will describe analysis workflows and considerations for detecting methylation
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Introduction to structural variation detection
This video will explain structural variation definitions, and introduce relevant file formats and detection workflows
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Introduction to de novo genome assembly and polishing
This video will introduce steps and workflows for the generation of high quality consensus genome sequences
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Introduction to read quality assessment and filtering
In this video you will learn about tools for assessing and filtering sequencing read data
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Data Analysis: EPI2ME Labs introduction
EPI2ME is a user-friendly analysis platform, highlighting best practice tools and analysis workflows for many applications. This video contains a short summary introducing the platform
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EPI2ME: RNA control experiment
This video explains how to run the FASTQ RNA Control Experiment workflow in EPI2ME to detect and assess RNA Calibration Strand (RCS) reads in nanopore sequencing datasets.
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EPI2ME Installation
Downloading and Installing EPI2ME
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Introduction to data analysis solutions
This video will provide an overview of data analysis solutions, resources and tutorials for the analysis of Nanopore data
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Introduction to data generation and sequencing output for analysis
Introduction to workflows and resources for the generation of read data from sequencing experiments and data files used for downstream analysis
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Running a Guppy basecalling script
In this video you will learn how to us the standalone version of Guppy to basecall nanopore sequencing data offline from the command line.
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SARS-CoV-2: ARTIC analysis workflow overview
The ARTIC network are a community of researchers that have developed robust analytical workflows for viral epidemiology and have made these workflows available through public repositories. These analysis resources can be used directly with sequencing data generated on your Nanopore device. In the case of the ARTIC Field Bioinformatics workflow, this can be used to identify SARS-CoV-2 variants and output consensus sequences for your sample
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Introduction: Real-time analysis
An introduction to portable, on-demand, real time sequencing with Oxford Nanopore Technologies
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Introduction to metagenomics classification concepts
This video introduces metagenomic classification and some of the key concepts necessary to help plan a successful metagenomic classification analysis workflow
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Technical demonstration of metagenomic classification through EPI2ME
This video demonstrates how to set up an What’s in My Pot (WIMP) analysis workflow in EPI2ME and explains the results provided
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Introduction to metagenomic classification solutions
This video introduces the metagenomic relevant workflows in EPI2ME and EPI2ME Labs and explains how they work and what the data outputs are
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Introduction to metagenomics
This video introduces the Metagenomics course and gives an overview of the flexible workflow options available to help plan and perform your metagenomics experiments.
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Additional concepts in metagenomic assembly
This video introduces additional concepts to help plan and perform metagenomic assembly analysis.
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Quality control of metagenomic assemblies
An overview into the concepts and tools you can use to assess the quality of your metagenomic assemblies.
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SARS-CoV-2: Midnight Protocol
Detailed run through the Midnight protocol with hints and tips for a successful library preparation.
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SARS-CoV-2: Eco ARTIC protocol
Detailed run through the Eco protocol with hints and tips for a successful library preparation.
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Library preparation: Ligation sequencing kit
Presenting the general workflow of the ligation sequencing kit, recommended input, options to scale-up, and the barcoding options available.
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SARS-CoV-2: Course Introduction
Introduction and background on SARS-CoV- 2 and the importance of whole-genome sequencing.
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SARS-CoV-2: Classic ARTIC protocol
Detailed run through the protocol with hints and tips for a successful library preparation.
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SARS-CoV-2: The ARTIC protocol and how it works
An introduction of the ARTIC protocol and how it works
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SARS-CoV-2: Options for whole genome sequencing protocols
An introduction to the different protocol options available to sequence SARS-CoV-2.
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MinKNOW: Installation
Learn about software releases, downloading and installing MinKNOW, and troubleshooting installation.
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SARS-CoV-2: Setting up a new ARTIC experiment
Demonstration on setting up a new experiment on the MinKNOW software.
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MinKNOW: Assessing your run
Tour through MinKNOW during a live run to understand the different graphs and assess the quality of your run.
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A practical demonstration of priming and loading a flow cell
Flow cell priming and sample loading demonstration
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MinKNOW: Flow cell check
Practical demonstration on how to complete the flow cell check using MinKNOW software.
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SARS-CoV-2: Secondary analysis post ARTIC analysis
There are a number of third-party web resources available to help you explore your data following the identification of variants and generation of a consensus sequence. In this video, you will learn about some of the available third-party websites that are available to help you explore your SARS-CoV-2 consensus sequence and variant data following the ARTIC analysis workflow
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SARS-CoV-2: ARTIC workflow data and analysis files
In this video we will introduce and discuss the main file types and file formats for the data files that are required and generated by the ARTIC Field Bioinformatics analysis workflow. This will explain the FASTQ, BAM, VCF and FASTA format files.
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SARS-CoV-2: EPI2ME Labs ARTIC analysis demonstration
The EPI2ME Labs platform can be used to perform analysis for several different applications. In this video, we will demonstrate the EPI2ME Labs workflow for analysis of your SARS-CoV-2 sequencing data, and highlight best practices when using the interface and and EPI2ME Labs analysis environment.
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SARS-CoV-2: ARTIC Field Bioinformatics analysis technical details
The ARTIC Field Bioinformatics workflow involves several analysis steps whereby data generated from a sequencing device is used to detect variants and generate a high-confidence consensus sequence. In this video we will explain the individual components and analysis software of this workflow
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MinION Mk1C unboxing and configuring
If you have bought a MinION Mk1C, in this video we show you the components included in the box. You will also learn how to power on the device and how to navigate the Mk1C Graphical User Interface.
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Guppy Introduction and Installation
In this video, you will learn about the features of Guppy and how to install it on Windows, Mac or Linux.
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Library Preparation: An introduction and overview of the options available
An overview of the various library preparation options available for our sequencing platforms.
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Library preparation: Quality control of input DNA or RNA
Outlining the importance of assessing your input DNA or RNA to maximise your sequencing run.
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MinKNOW: Blocking
Using the MinKNOW GUI to identify and troubleshoot blocking during a sequencing run
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Library preparation: Extraction methods and sample handling
Containing resources available for advice on sample extraction and recommendations for DNA and RNA handling.
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Library preparation: Improving sequencing yields
Presenting the most important aspects of the library preparation chemistries and how to improve performance whether it's high throughput or longer reads.
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Library preparation: Barcoding kits and workflows
Presenting the barcoding kits and workflows available for nanopore sequencing
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Library preparation: 16S barcoding kits
Targeted metagenomic approach and how to perform real-time downstream analysis of your data using the cloud-based FastQ 16S workflow in the Epi2me platform.
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Library preparation: Low input PCR kits
Library preparation options using low input DNA kits
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Library preparation: Rapid sequencing kits
Presenting rapid sequencing of genomic DNA using the Rapid Sequencing kits
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Library Preparation: Comparing PCR-free kits
Comparison of PCR-free chemistries, ligation and rapid sequencing kits and the advantages of PCR free applications in Whole genome, Metagenomic and Epigenetics sequencing.
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MinKNOW: Post-run analysis
Learn about the main post-run analysis processes performed by MinKNOW
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MinKNOW: Translocation speed
Understand translocation speed and how to identify and troubleshoot translocation speed changes
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MinKNOW: Re-using a flow cell
The wash kit explained, how to adjust bias voltage when reusing a flow cell in MinKNOW.
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MinKNOW: Setting up a new experiment
Demonstration on setting up a new experiment on the MinKNOW software.
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MinKNOW: The graphical user interface (GUI)
Guided tour through MinKNOW's graphical user interface
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MinKNOW: Live basecalling and output folder structure
Set up live basecalling in MinKNOW and chose basecalling model. Introduction to data file types and folder structure.
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MinKNOW: Mux scan and active channel selection
Introduction to MUX scan and active channel selection.
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MinKNOW: Pore occupancy
Introduction to pore occupancy, how to monitor and interpret this during a run, and how to troubleshoot for different scenarios.
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Knowledge Exchange: The EPI2ME Labs structural variation tutorial – an extensible framework for SV detection, QC, and visualisation
EPI2ME Labs is an emerging Oxford Nanopore product that introduces best practise and literate bioinformatics workflows. The workflows are packaged as follow-along tutorials and are provided with example datasets.
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Knowledge Exchange: Structural variation
This Knowledge Exchange provides an overview of structural variation detection using long reads.
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Knowledge Exchange: cDNA sequencing on the Oxford Nanopore platform
This Knowledge Exchange introduces cDNA sequencing with Oxford Nanopore technology - from library prep to analysis.
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Knowledge Exchange: Library preparation kits and methods
This Knowledge Exchange covers the essentials of sample and library preparation for Oxford Nanopore Technologies sequencing devices.
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Knowledge Exchange: Getting the most out of a flow cell
This Knowledge Exchange provides top tips for getting the most out of a nanopore sequencing flow cell.
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Knowledge Exchange: MinKNOW features and updates
This Knowledge Exchange provides an overview of the latest MinKNOW features.
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Knowledge Exchange: Sample barcoding
This Knowledge Exchange provides an overview of the Oxford Nanopore barcoding kits available.
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Knowledge Exchange: Assembly
With the increasing yield of the Oxford Nanopore platform, it’s becoming easier to generate enough data to assemble large genomes. In this Knowledge Exchange, learn how to plan and perform genome assembly projects using nanopore sequencing.
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