Technical resources for the MiSeq

A comprehensive list of resources needed to set up, operate, maintain, and troubleshoot the MiSeq sequencing system is on the MiSeq Support page. Specific documentation links are found below.
MiSeq Sequencing Welcome Card Graphical introduction to the MiSeq System.
MiSeq Sample Sheet Quick Reference Guide Guidance for setting up sample sheets for sequencing on the MiSeq.
MiSeq Run Folder Quick Reference Card Instructions for using the MiSeq output and analysis folders.
MiSeq System Specification Sheet Contains basic information including output and time specifications for the MiSeq.
MiSeq System Specification Page Provides the data quality and yield specifications for the MiSeq.
MiSeq Sequencing System Site Prep Guide Contains lab requirements, networking guidelines, and security considerations.
MiSeq System Guide for MiSeq Reporter Contains a workflow overview, maintenance procedures, and troubleshooting resources for MiSeq systems running MCS v2.6 and below.
MiSeq System Guide for Local Run Manager Contains a workflow overview, maintenance procedures, and troubleshooting resources for MiSeq systems running MCS v3.1 and greater.
Local Run Manager Support Resources Contains on- and off-instrument versions of Local Run Manager.
MiSeq System Custom Primers Guide Contains instructions for preparing and loading custom primers and editing the sample sheet when using custom primers on a MiSeq run.
MiSeq System Denature and Dilute Libraries Guide Contains instructions for preparing PhiX and denaturing and diluting libraries for sequencing on the MiSeq.
Cluster Optimization Overview Guide Describes strategies for optimizing cluster density and preventing and diagnosing clustering issues on Illumina flow cells.
Low-Diversity Sequencing on the Illumina MiSeq Platform Describes changes when using RTA version 1.17.28 with low diversity samples in newer versions of MiSeq Control Software (MCS).
MiSeq System Frequently Asked Questions Answers to commonly asked questions about running on a MiSeq system.
Online Training Courses Online trainings and recorded webinars include
  • video courses on preparing for instrument installation
  • how to start a run
  • how to perform instrument washes
  • how to set up / view analysis results on Local Run Manager
To access additional online training courses, navigate to the Training website, and under Filters select Training Type > Training and Videos > Online Training
Safety Data Sheets Safety Data Sheets contain information to help with appropriate reagent disposal practices. To obtain this information, enter the kit catalog number, language, and region/country, then select Search.
Additional technical resources are available 24/7 at the MiSeq Sequencing System Support website.
For any feedback or questions regarding this article (Illumina Knowledge Article #7486), contact Illumina Technical Support [email protected].
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