HiSeq 2500 Training

  • Introductory Topics


  • 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: 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.

  • 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

  • Instruments & Software


  • HiSeq 1500/2500: Best Practices

    This course covers best practices for your HiSeq 1500/2500. Topics covered include: instrument mode changes and washes, best practices for performing a HiSeq sequencing run, BaseSpace Sequence Hub and data compression options for your HiSeq runs, fluidics and flow cell plate care, and how to prepare the instrument for idling or shutdown.

    25 min

  • HiSeq: Rapid Run Mode

    This course describes the Rapid Run Mode available for HiSeq 2500 or HiSeq 1500. It identifies what is needed to perform a Rapid Run, describes the options for clustering the 2-lane flow cell, and lists ways to reduce data storage requirements for your HiSeq runs.

    15 min

  • 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

  • HiSeq Expert Video Tips Part 1: Sequencing Primers

    This video discusses how to choose the appropriate sequencing primers for your run. Since commonly used Illumina indexes, TruSeq™ and Nextera™, utilize different index primer site sequences, it's important that the correct primer is loaded into the HiSeq for sequencing.

    3 min

  • HiSeq Expert Video Tips Part 2: Instrument Computer Tips

    This video offers tips and troubleshooting advice related to the HiSeq Instrument computer, including navigating the instrument's Port Manager, formatting hard drives, and setting up a second run.

    7 min

  • HiSeq Expert Video Tips Part 3: Mechanical System, Thermal System, and Maintenance Best Practices

    This video offers tips on the mechanical and thermal systems of the HiSeq, as well as best practices on maintaining your instrument.

    7 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

  • HiSeq Expert Video Tips Part 4: Tips for Proper Fluidics Flow

    This video introduces the fluidics system. Topics include fluidics leaks, syringe pump function, and priming the HiSeq 2500 template loading station.

    9 min

  • HiSeq Expert Video Tips Part 5: Removing Fluidic Line Blockages

    This video continues to share tips and tricks for the fluidics system started in Part 4 of the series. The video focuses on how to identify and remove blockages from the fluidics lines to ensure the HiSeq instrument is used at its highest capacity.

    7 min

  • 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

  • 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