For the installers for Local Run Manager and Local Run Manager analysis modules, see Local Run Manager Downloads.

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MiSeq Software Updater

For details about MiSeq Software Updater v3.0, see the MiSeq Software v3.0 Release Notes. For full installation instruction, see the Installation Notes included in the Updater download package. This software release continues to use the Reference Genomes v1.1.0.0 for MiSeq. If you have previously installed this version of the Reference Genomes, there is no need to update the genomes again.

Note: The software updater can also be installed in the RUO drive of MiSeqDx instruments with dual boot configuration. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support. 

MiSeq Software Release Notes

MiSeq software release notes describe features and changes introduced in the latest versions of MiSeq Control Software (MCS) and related software components, including MiSeq Reporter.

MiSeq Reporter Installer

MiSeq Reporter is the bioinformatics data analysis software built into the MiSeq. MiSeq Reporter is available as a standalone software for installation on a US–English, 64–bit Windows workstation. See Computing Requirements.

For installation of MiSeq Reporter, see the Install Supporting Microsoft Files section of the MiSeq Reporter Software Guide.

MCS v2.2.2 Optional Hotfix

Use the MCS v2.2.2 optional hotfix for instruments that consistently show a chiller temperature higher than 6°C (6.00 C). The following download includes the MCS v2.2.2 installer, installation notes, and release notes.

bcl2fastq2 Conversion Software v2.20

This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2.20.0, which can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. This software requires a Linux operating system.

The bcl2fastq2 Conversion Software v2.20.0 can be used to convert BCL files from MiniSeq, MiSeq, NextSeq, HiSeq, iSeq and NovaSeq sequening systems. For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4.

The software is available as an RPM (*.rpm) for installation on CentOS/RedHat Linux distributions. A tarball (*.tar.gz) of the source code is also available for compilation on other Linux distributions. Installation instructions are provided in the Software Guide.

Sequencing Analysis Viewer v2.4.5 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiniSeq, MiSeq (with MCS v2.6.2 and higher), NextSeq, HiScanSQ, all HiSeq systems, and NovaSeq. Download and unzip this file to install SAV for viewing sequencing runs on an offline computer. This SAV version requires Windows .NET Framework 4.5.1 and Visual C++ Redistributable for Visual Studio 2015. If your system is using Windows .NET Framework 4 or you are running a MiSeq with MiSeq Control Software v2.5 and lower, continue using SAV 1.8.37.