MiSeq Training

  • Introductory Topics


  • 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

  • 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: Introduction to Sequencing By Synthesis (SBS)

    Recorded Webinar (June 2020) | 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 Analysis Viewer (SAV): A Beginner's Guide

    Recorded Webinar (May 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.

  • Library Prep


  • 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

    Recorded Webinar (January 2020)| 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.

  • Instruments & Software


  • 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

  • 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.

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

    20 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: An overview of metagenomics, library preparation strategies and considerations, sequencing options, run performance evaluation, and data analysis workflows.

    Jul 21, 2020 PST

  • Data Analysis


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

    Recorded Webinar (December 2019) | 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.

  • Optimal Cluster Density Best Practices

    This video discusses optimal cluster density and how over and under-clustering can affect your sequencing data. It also examines common clustering issues and ways to prevent them.

    10 min

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

    Upcoming Webinar | El programa “Sequencing Analysis Viewer” (SAV) es una aplicación gratuita para ver importantes métricas de calidad generadas durante la secuenciación. Esta videoconferencia proporcionará una visita guiada para principiantes sobre cómo usar SAV, así como consejos para evaluar la información más pertinente al control de calidad. Esta presentación está dirigida a nuevos usuarios y cubrirá los siguientes temas: Cómo importar datos a SAV, Qué métricas están disponibles en cada pestaña del software, Comprender cuáles son las métricas más valiosas para la revisión de una corrida y dónde encontrarlas.

    Jul 22, 2020 PST