HiSeq 4000 Training

  • Introductory Topics

    DATE/LENGTH


  • 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), French,

    15 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.


  • 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)

    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 Preparation

    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


  • 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


  • 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.


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

    Recorded Webinar (November 2019) | 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 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