Local Run Manager Training

  • Title

    DATE/LENGTH


  • 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


  • 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


  • 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


  • 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


  • BaseSpace Sequence Hub: FASTQ Processing Tools for Data Analysis

    Recorded Webinar (August 2020) | FASTQ files store biological sequence and quality information and are key for downstream data analysis pipelines. Several steps are necessary during FASTQ generation to ensure optimal data analysis. This webinar is targeted at new and intermediate users including biologists intending to understand output of basic bioinformatics tools used for processing FASTQs. We will focus on BaseSpace Sequence Hub tools such as FASTQC and FASTQ toolkit*. 

    We will cover the following topics: What is a FASTQ file; An overview of Illumina FASTQ generation tools; FASTQ processing such as adapter trimming, masking, quality trimming, read stitching etc; and Highlight the differences between Illumina run performance metrics and output generated by third party tools such as FASTQC.

    *BaseSpace Labs Apps are developed using an accelerated development process in order to make them available to BaseSpace users faster than conventional Illumina Apps. Illumina may provide support for BaseSpace labs Apps at its sole discretion. BaseSpace Labs Apps are provided AS-IS without any warranty of any kind. BaseSpace Labs Apps are used at the user’s sole risk. Illumina is not responsible for any loss of data, incorrect results, or any costs, liabilities, or damages that may result from the use of a BaseSpace Labs App.


  • 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


  • NextSeq 550: How to Start a Run

    By the end of this course, you will be able to: identify the steps to start a run on the NextSeq 550, describe how to prepare the reagent cartridge, and start a sequencing run using NCS.

    20 min


  • NextSeq 550: Run Quality and Best Practices

    Recorded Webinar (May 2021) | Evaluating the quality of data produced by your run and making adjustments for ideal output is an important part of the sequencing process. This webinar is targeted to newer users of the NextSeq 550 sequencing platform, reviewing problem phenotypes and the underlying causes. We will address the following topics: The basic mechanics of the NextSeq 550 System and NextSeq 2-color chemistry; Expected data output from NextSeq 550 runs; Changes with the upgrade to NextSeq Control Software v4.0; The important data that we can glean from Sequence Analysis Viewer; Several common problem phenotypes and how to diagnose them.