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


  • MiSeq: Preparing for Your Install

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

    Languages: Chinese (Simplified), German, Japanese, Korean, Spanish

    20 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 (January 2021) | 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.


  • Bcl2Fastq v2+: Introduction

    Recorded Webinar (April 2019) | Bcl2Fastq is a Linux-based software that converts base call files generated from an Illumina sequencing run to FASTQ files as well as demultiplex samples. This webinar focuses on Bcl2fastq v2+ and is targeted for new to intermediate users who are interested in the configurable options that this command line program allows. We will cover the following topics: requirements to run Bcl2Fastq, command line basics, commonly used options, frequently asked ‘How To….’ questions.


  • Sequencing Analysis Viewer (SAV): A Beginner's Guide

    Recorded Webinar (December 2020) | The Sequencing Analysis Viewer (SAV) Software is an application where users can view important quality metrics generated during sequencing runs. This webinar will provide a guided tour for beginners on how to use SAV, as well as tips and tricks for reviewing the most useful information for sequencing runs. This webinar is targeted at new users and will go over the following topics: how to load data into SAV, what metrics are available in each tab of the software, and understanding which are the most valuable metrics for run review and where to find them.


  • Sequencing: Illumina Technology

    This course provides a general overview of the Illumina sequencing workflow from extraction of nucleic acids to the completion of a sequencing run.

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

    15 min


  • 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


  • Amplicon Sequencing: Introduction

    Recorded Webinar (May 2021)| 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.


  • Illumina DNA Prep Library Preparation

    By the end of this course, you will be able to identify the Illumina DNA Prep 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


  • 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).

    Languages: Chinese (Simplified), German, Japanese, Korean, Spanish

    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).

    Languages: Chinese (Simplified), German, Japanese, Korean, Spanish

    20 min


  • Local Run Manager v2

    This course shows you how to get started using the Local Run Manager v2 software to set up your sequencing runs and view analysis results. Local Run Manager v2 is available for MiniSeq instruments using MiniSeq Control Software v2 or later, NextSeq 500/550 instruments using NextSeq Control Software v4 and later, and MiSeq instruments using MiSeq Control Software v3.

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

    20 min


  • Diagnosing Suboptimal Clustering in Nonpatterned Flow Cells

    Learn which run metrics and thumbnail images to monitor during a run to diagnose over clustering of a nonpatterned flow cell.

    8 min


  • Local Run Manager v3

    This course shows you how to get started using the Local Run Manager v3 software to set up your sequencing runs and view analysis results. Local Run Manager v3 is available for MiSeq instruments using MiSeq Control Software v4 and later.

    Languages: Chinese (Simplified), German, Japanese, Korean, Spanish

    20 min


  • Local Run Manager v3 with MiSeq Control Software v4: Introduction

    Recorded Webinar (February 2021) | Launching with the MiSeq Windows 10 update and MiSeq Control Software version 4, Local Run Manager version 3 is the Windows-based software solution for run management and data analysis. Local Run Manager v3 replaces MiSeq Reporter, and this webinar provides an introduction to the features of Local Run Manager v3. We will cover the following topics: features of Local Run Manager v3, how to set up runs and analyze data, available analysis workflows, and interaction with MiSeq Control Software V4


  • Metagenomics Part II: Introduction to Analysis

    Recorded Webinar (March 2021) | Following Metagenomics Sequencing Part I, in this webinar, we will discuss Introduction to Data Analysis in Metagenomics. We assume a basic understanding of Illumina sequencing technology and knowledge of library prep workflow for Metagenomics. We will discuss the following topics: Overview of Targeted Metagenomics and Shotgun Metagenomics, Options for Metagenomics Data Analysis:  16s Metagenomics App and DRAGEN metagenomics Pipeline on BaseSpace Sequence Hub, and Overview of DRAGEN RNA Pathogen Detection App on BaseSpace Sequence Hub.


  • MiSeq: Preparing for Your Install

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

    Languages: Chinese (Simplified), German, Japanese, Korean, Spanish

    20 min


  • 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: 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.

    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. MiSeq Reporter is available on instruments using MiSeq Control Software v2.6 and earlier.

    25 min


  • BaseSpace Sequence Hub: Introduction and Analysis Overview

    Recorded Webinar (May 2020) | 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.


  • Diagnosing Suboptimal Clustering in Nonpatterned Flow Cells

    Learn which run metrics and thumbnail images to monitor during a run to diagnose over clustering of a nonpatterned flow cell.

    8 min


  • Local Run Manager v2 (Research Use Only): Introduction - On- and Off-Instrument

    Recorded Webinar (January 2021) | 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. It will provide an overview of the Research Use Only (RUO) version of Local Run Manager v2 including the off-instrument version and the versions bundled with instrument control software. This webinar does not cover the Dx versions of the software. We cover the following topics: features of Local Run Manager v2, 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.


  • Local Run Manager v3 with MiSeq Control Software v4: Introduction

    Recorded Webinar (February 2021) | Launching with the MiSeq Windows 10 update and MiSeq Control Software version 4, Local Run Manager version 3 is the Windows-based software solution for run management and data analysis. Local Run Manager v3 replaces MiSeq Reporter, and this webinar provides an introduction to the features of Local Run Manager v3. We will cover the following topics: features of Local Run Manager v3, how to set up runs and analyze data, available analysis workflows, and interaction with MiSeq Control Software V4


  • Sequence Analysis Viewer (SAV): A Beginner's Guide

    Upcoming Webinar | The Sequencing Analysis Viewer (SAV) Software is an application to view important quality metrics generated during sequencing runs. This webinar will provide a guided tour for beginners on how to use SAV, as well as tips and tricks for reviewing the most useful information for sequencing runs. This webinar is targeted at new users and will go over the following topics: How to load data into SAV, what metrics are available in each tab of the software, and understanding which are the most valuable metrics for run review and where to find them.

    Sep 23, 2021 PST


  • Sequencing Analysis Viewer (SAV): A Beginner’s Guide (Portuguese)

    Upcoming Webinar | O software Sequencing Analysis Viewer (SAV) é um aplicativo para visualizar importantes métricas de qualidade geradas durante as corridas de sequenciamento genético. Este webinar fornecerá um tour guiado para iniciantes sobre como usar o SAV, bem como dicas e truques para revisar as informações mais úteis das corridas de sequenciamento genético. Este webinar é direcionado para novos usuários e abordará os seguintes tópicos: Como carregar dados no SAV, quais métricas estão disponíveis em cada aba do software, compreender quais são as métricas mais valiosas para a revisão de uma corrida e onde encontrá-las.

    Aug 11, 2021 PST