MiniSeq Training

  • Introductory Courses


  • 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

  • MiniSeq: Introduction

    Recorded Webinar (September 2016) | Please join us for a technical presentation the MiniSeq benchtop sequencer. This webinar will educate new and experienced Next-Generation Sequencing users to how this system works, its new features, how dual indexing is performed, best practices and introductory guidance on run analysis.

  • MiniSeq: Preparing for Your Install

    By the end of this course, you will be able to list the key components of the MiniSeq System, describe the lab environment required to install and use the MiniSeq System, and identify the user-supplied consumables required for running and maintaining the instrument.

    15 min

  • MiniSeq: System Overview

    By the end of this course, you will be able to identify features of the MiniSeq System, describe MiniSeq sequencing technology, and describe the simplified sequencing workflow of the MiniSeq System.

    20 min

  • 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


  • 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.

  • Instruments & Software


  • 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

  • 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

  • Local Run Manager v1

    This course provides an introduction to the Local Run Manager v1 software for MiniSeq instruments using MiniSeq Control Software v1. Topics include: its purpose, how to access the software, and the analysis workflows. It also shows the steps to set up a sequencing run and view analysis results.

    15 min

  • 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.

  • MiniSeq: Does My Run Look Good?

    This course explores the options for monitoring your MiniSeq run. Also detailed are the key metrics in MiniSeq Control Software, Sequencing Analysis Viewer, and BaseSpace Sequence Hub.

    10 min

  • MiniSeq: How to Start a Run

    This course provides an overview of how to set up and start a sequencing run on the MiniSeq System.

    20 min

  • 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

  • Data Analysis


  • 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