MiSeq Training

  • Introductory Topics

    DATE/LENGTH


  • Sequencing: Fundamentals

    After completing this course you will be able to describe DNA, RNA and the central dogma; discuss traditional sequencing methodologies; and compare traditional sequencing to sequencing by synthesis.

    Languages: French, Italian, German, SpanishChinese (Simplified)

    15 min


  • How Do I Prepare for My Illumina Instrument Delivery?

    In this video, an Illumina Field Applications Scientist discusses what to expect during the pre-installation, shipping, and delivery stages. We’ll highlight important steps in the process and introduce you to available resources. Note that, depending on your region, the steps shown in this video may not apply to the iSeq 100 system.

    7 min


  • Sequencing: Introduction to Sequencing By Synthesis (SBS)

    Recorded Webinar (July 2019) | Illumina next-generation sequencing technology allows for massive parallel sequencing. Illumina Technical Support invites you to join us for a presentation and discussion on sample preparation, cluster generation and sequencing by synthesis chemistry. This webinar is targeted to those new to next-generation sequencing and will discuss the following topics: Illumina library construction, cluster generation methods by platform, sequencing by synthesis, and multiplexing and primary analysis.


  • Sequencing: Introduction to Sequencing By Synthesis (SBS) - Brazil (Português)

    Upcoming Webinar | A tecnologia Illumina de sequenciamento de nova geração permite o sequenciamento em larga escala e alta profundidade. O Suporte Técnico da Illumina convida você para juntar-se a nós em uma apresentação e discussão sobre o preparo de biblioteca, clusterização e a química de sequenciamento por síntese. Esse webinar é direcionado a novos usuários da tecnologia de sequenciamento de nova geração e serão discutidos os tópicos abaixo: Construção de biblioteca Illumina, métodos de clusterização por plataforma, sequenciamento por síntese, e multiplexing e análise primária.

    Nota: Apresentação oral às 2:00 pm (Brasilia Time)

    Nov 26, 2019 PST


  • Sequencing: Introduction to Sequencing By Synthesis (SBS)

    Upcoming Webinar | Illumina next-generation sequencing technology allows for massive parallel sequencing. Illumina Technical Support invites you to join us for a presentation and discussion on sample preparation, cluster generation and sequencing by synthesis chemistry. This webinar is targeted to those new to next-generation sequencing and will discuss the following topics: Illumina library construction, cluster generation methods by platform, sequencing by synthesis, and multiplexing and primary analysis.

    Jan 09, 2020 PST


  • Library Prep

    DATE/LENGTH


  • Illumina Experiment Manager

    This course provides an introduction to Illumina Experiment Manager, and shows you the steps to create sample plates and sample sheets.

    25 min


  • AmpliSeq for Illumina: Library Prep Protocol

    This course identifies the items needed for the AmpliSeq for Illumina library prep protocol, introduces pool planning resources for a multiplexed amplicon run, demonstrates the steps in the library prep protocol, and lists best practices for the protocol.

    30 min


  • AmpliSeq for Illumina: Overview

    This course describes the AmpliSeq for Illumina assay technology, lists the three types of panels, introduces the steps in the amplicon sequencing workflow, and lists the analysis options for amplicon sequencing data.

    15 min


  • Nextera DNA Flex Library Preparation

    By the end of this course, you will be able to identify the Nextera DNA Flex kit, describe how the protocol works, identify what is needed to complete the protocol, and define the various steps in the library preparation workflow.

    20 min


  • Amplicon Sequencing: Introduction

    Upcoming Webinar | Illumina Technical Support invites you to join us to discuss the end-to-end workflow for an amplicon sequencing project. This webinar is ideal for new users of Illumina Next Generation Sequencing. We will discuss amplicon sequencing, including the following topics: what defines an amplicon library, kits and protocols for amplicon libraries, and amplicon sequencing runs and parameters.

    Jan 30, 2020 PST


  • Instruments & Software

    DATE/LENGTH


  • Discover the Benefits of Illumina Proactive

    Learn about the benefits of instrument performance monitoring through Illumina Proactive, a service in which instrument performance data are sent to Illumina to enable proactive maintenance.

    10 min


  • IT Requirements for Implementing Illumina Proactive

    This video shares IT requirements for implementing Illumina Proactive, an instrument performance monitoring service provided by Illumina that can increase instrument uptime, improve operational efficiency, and reduce the risk of lost resources.

    4 min


  • MiSeq: How to Start a Run

    After completing this course you will be able to identify the MiSeq run setup options, describe how to prepare the MiSeq reagent cartridge and load libraries, and list the steps to start a sequencing run with MiSeq Control Software (MCS).

    20 min


  • MiSeq: Instrument Washes

    This course provides an overview of the three MiSeq instrument washes: the post-run wash, the maintenance wash, and the standby wash.

    Languages: Spanish, Chinese (Simplified), Japanese

    10 min


  • MiSeq: Preparing for Your Install

    After completing this course you will be able to describe the lab environment required to use MiSeq, list key components of MiSeq, identify the network considerations for MiSeq, and list the user-supplied consumables required for running and maintaining MiSeq.

    20 min


  • MiSeq: Does My Run Look Good?

    After completing this course you will be able to list two options for monitoring your MiSeq run, describe key metrics in MiSeq Control Software (MCS), and describe key metrics in Sequencing Analysis Viewer (SAV).

    10 min


  • Metagenomics Sequencing: Introduction

    Upcoming Webinar | Illumina Technical Support invites you to join us to discuss the end-to-end workflow for a metagenomics sequencing project. This webinar is ideal for new and intermediate users of Illumina Next Generation Sequencing with an interest in metagenomics. We will discuss targeted metagenomics and shotgun metagenomics sequencing, including the following topics: overview of metagenomics, library preparation strategies and considerations, sequencing options, run performance evaluation, and data analysis workflows.

    Jan 16, 2020 PST


  • MiSeq: Run Quality and Troubleshooting

    Upcoming Webinar | Illumina Technical Support invites users to join us for a discussion of the MiSeq system. The MiSeq System offers integrated cluster generation, amplification, sequencing, and data analysis into a single instrument. This webinar will go through troubleshooting considerations at each of these steps, and is targeted toward new and intermediate users with a basic understanding of the Illumina sequencing workflow and the Sequence Analysis Viewer (SAV) software. We will review troubleshooting Run Setup and Run Start, assessment of runs in progress using SAV, and tips and best practices.

    Dec 05, 2019 PST


  • Data Analysis

    DATE/LENGTH


  • How Can I Tell If I Sequenced Through the Insert? Part 1

    An Illumina Field Applications Scientist describes what it means to sequence through the insert of your prepared library. We look at Bioanalyzer traces to assess the range of insert sizes in a library.

    7 min


  • How Can I Tell If I Sequenced Through the Insert? Part 2

    This video shows you how to use Sequencing Analysis Viewer (SAV) plots to determine if your sequencing insert is too short. We also explore how to use the adaptertrimming.txt file on the MiSeq to diagnose short inserts.

    5 min


  • Is My HiSeq or MiSeq Run Overclustered?

    This video provides an overview of overclustering and how it can impact your sequencing data. An Illumina Field Applications Scientist shows you how to use Sequencing Analysis Viewer (SAV) to look for common symptoms of an overclustered HiSeq or MiSeq flow cell.

    7 min


  • MiSeq: Data Analysis Overview

    After completing this course you will be able to list the MiSeq data analysis tools, briefly describe the function of each tool, and list some considerations when choosing your MiSeq data analysis tool.

    Languages: SpanishJapanese

    10 min


  • MiSeq: Imaging and Base Calling

    After completing this course you will have an understanding of how the MiSeq processes images to extract intensities and processes intensities to extract base calls.  These processes are completed automatically by the MiSeq.

    Languages: Spanish, Chinese (Simplified), Japanese

    35 min


  • MiSeq: MiSeq Reporter

    After completing this course you will have an understanding of the demultiplexing and alignment processes and program interfaces that are common to all workflows in MiSeq Reporter. You will also be able to briefly describe the utility of the supported MiSeq Reporter workflows.

    Languages: Spanish, Chinese (Simplified), Japanese

    25 min


  • BaseSpace Sequence Hub: Introduction and Analysis Overview

    Recorded Webinar (September 2019) | llumina Technical Support invites you to learn about BaseSpace, Illumina’s cloud-based sequencing data analysis solution. In this presentation, we will discuss how to navigate the BaseSpace dashboard, general BaseSpace functionally, and tips and tricks for successful application and workflow utilization. We will cover the following topics: How to upload/view data in BaseSpace, discussion of major analysis workflows, general overview of how to analyze data on BaseSpace.

    Please note: BaseMount and BaseSpace CLI are alpha software releases; features and functionality may change over time, and support is directly through Illumina software development.


  • Local Run Manager 2.0 (Research Use Only): Introduction - On- and Off-Instrument

    Upcoming Webinar | Local Run Manager is a Windows-based software for Illumina benchtop sequencing data that includes local analysis options as well as run and user management. This webinar targets new and intermediate users of the software. It will provide an overview of the Research Use Only (RUO) version of Local Run Manager 2, including the off-instrument version and the versions bundled with the latest MiSeq Control Software, iSeq Control Software, and NextSeq Control Software. This webinar does not cover the Dx versions of the software. We will cover the following topics: Features of Local Run Manager 2, available versions and analysis options, how to set up runs and analyze data, interaction with on-instrument control software, and comparison to other Illumina analysis software.

    Dec 17, 2019 PST


  • Sequencing Considerations for Low Diversity Libraries

    Upcoming Webinar | Low diversity libraries, such as those used for amplicon sequencing, can present challenges on Illumina sequencing systems and may skew software performance and data accuracy resulting in poor quality runs. This webinar is ideal for new and intermediate users interested in considerations for the sequencing of low diversity libraries and will cover the following topics: understanding and visualizing base diversity in Sequencing Analysis Viewer (SAV), strategies to optimize low diversity sequencing data, % PhiX spike-in and cluster density recommendations for different sequencing platforms, and an overview of base calling and quality score calculations.

    Jan 23, 2020 PST