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, go 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 handling and 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.