Local Run Manager on NextSeq

As part of the upgrade to NextSeq Control Software (NCS) v4, the NextSeq system will receive Local Run Manager, an integrated software solution for managing sequencing runs. Local Run Manager integrates with instrument control software and can be accessed directly on a NextSeq System or run remotely.

Local Run Manager enables a streamlined, user-friendly interface for setting up samples, runs, and analysis, and for viewing analysis results. It also supports importing and exporting sample sheets. User management includes permission setup and an audit trail. Multiple analysis modules for analyzing various library types are available for use with Local Run Manager.


Local Run Manager is part of the instrument software suite and does not require separate installation.

If your instrument is connected to the internet, you can download the module file and install it directly onto the Local Run Manager system. Analysis modules are downloaded separately via the Local Run Manager software downloads page on the Illumina support website.

Analysis Modules

Local Run Manager supports the below analysis modules.* The reference guide for each module describes the analysis pipelines on which the module is based.

  • 16S Metagenomics Analysis Module
  • Amplicon DS Analysis Module
  • Assembly Analysis Module
  • DNA Amplicon Analysis Module
  • DNA Enrichment Analysis Module
  • GenerateFASTQ Analysis Module
  • Library QC Analysis Module
  • Amplicon Module
  • Resequencing Analysis Module
  • RNA Amplicon Analysis Module
  • RNA Fusion Analysis Module
  • Small RNA Analysis Module

* Additionally, there are a variety of third-party analysis solutions available, each with a unique set of capabilities and limitations. It is recommended that potential solutions be assessed on a per-project basis to determine best fit.

Using Previously Generated Prep Tab Data

With the upgrade to NCS v4, uploading projects to BaseSpace Sequence Hub requires you to set up runs in Local Run Manager rather than in Prep tab. Data generated on BaseSpace Sequence Hub using Prep tab versus Local Run Manager for run setup are equivalent. If you plan to use Local Run Manager on-instrument, we recommend that you directly compare output with previous data generated via Prep tab, as on-instrument and cloud-based analysis may differ for some modules.

Additional Resources

Technical Bulletins