Local Run Manager Software

This page supports on- and off-instrument versions of Local Run Manager. If you sequence AmpliSeq for Illumina panels on the MiniSeq System, visit Local Run Manager for the MiniSeq System Support.


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Custom Protocol Selector

Generate end-to-end documentation tailored to your experiment.

Library Prep and Array Kit Selector

Determine the best kit for your project type, starting material, and method or application.

Sequencing Coverage Calculator

Determine reagents and sequencing runs for your desired coverage.


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Maximize the effectiveness of your Illumina system, train new employees, or learn the latest techniques and best practices. We offer support webinars, online courses, expert video tips, and instructor-led trainings.

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Local Run Manager

How to get started using the Local Run Manager software to set up your sequencing runs and view analysis results.

FASTQ Processing Tools for Data Analysis

Details the basic bioinformatics tools used for processing FASTQs.

Local Run Manager 2.0 (RUO) - MiSeq, iSeq 100, and Off-Instrument

Overview of software features, available versions, run setup steps, and comparison to other Illumina analysis software.