Sequencing Downloads

*The downloadable materials displayed on this web page are proprietary to Illumina, Inc., and are intended solely for the use of its customers and for no other purpose than use with Illumina's products or services. The downloadable materials and their contents shall not be used or distributed for any other purpose or otherwise communicated, disclosed, or reproduced in any way without the prior written consent of Illumina, Inc.

You can download current software and support files by clicking one of the links listed below. The description expands to show available downloads. Click the desired download and select Save. If you are looking for documentation, visit the Sequencing Documentation page.

Description
 
File Info
Date
HCS 2.2.68 Software for HiSeq 2500, 2000, 1500, and 1000 Systems

This download contains an update to the HiSeq Software Suite and includes new versions of HiSeq Control Software (HCS), Real-Time Analysis (RTA), Batch Installer, and the BaseSpace Broker. This software includes support for BaseSpace Onsite (BSO) functionality. BaseSpace v2.0 is required. Download and review the customer release notes for details about this release.

Nextera Rapid Capture Exome Unique Intervals File

"This download contains the Nextera Rapid Capture Exome target region intervals that do not overlap the Nextera Rapid Capture Expanded Exome target regions. There are a total of 4.1 MB that are unique to the Exome product. 336,295 intervals across 205,598 Exome targeted regions. This was determined by base overlap only. For example, comparing an Exome product region at Chr 1 position 300 – 500 with an Expanded Exome region at Chr 1 position 305 – 495 results in a 191 bp overlap and two 5 bp ""unique regions"" for the Exome product."

Beeline Software v2.0.1

This download includes release notes and installers for the Beeline Software v2.0.1 and AutoConvert Software v2.0.

Nextera Rapid Capture Exome Product Files

This download contains the Nextera Rapid Capture Exome targeted regions manifest files (.txt and .bed), and the exome probe manifest. The targeted regions manifest files list the 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19. The exome probe manifest file lists the 412,006 enrichment probes with chromosome location in GRCh37/hg19.

The Nextera Rapid Capture Exome Targeted Regions Manifest and the Nextera Rapid Capture Exome Probe Manifest files are in .txt format. This format is required by the HiSeq Analysis Software.

TruSight Autism Content Set Product Files

 

This manifest file contains the list of targeted regions corresponding to the TruSight Autism Content Set. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of TruSight Autism set.

This bed file contains information on the TruSight Autism Content Set. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information.

Note regarding biomarker patents and other patents unique to specific uses of products.

Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents. Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application.

 

Illumina no longer accepts orders for TruSight Autism. The recommended replacement product is the TruSight One Sequencing Kit. Content from the TruSight Autism panel is avaialble in the comprehensive TruSight One Sequencing Panel. Illumina remains committed to providing you with high-quality support and service.
cBot Software v1.5 Installer

This download contains the installers for cBot software. cBot software v1.5 provides rapid run recipes required for rapid run chemistry and flow cells. cBot software v1.4 provides v8 recipes required for v3 chemistry and flow cells. For additional details, please review the release notes and installation notes before installation.

Sequencing Analysis Viewer v1.11 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiniSeq, MiSeq (with MCS v2.6.2 and higher), NextSeq, HiScanSQ, HiSeq X, and all HiSeq systems. 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. 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.

cBot Software v3.0.46 Installer

This download contains the installer for the cBot software v3.0.46, which includes recipes required for the HiSeq 3000/4000 SR Cluster Kit. This software is for the cBot 2 and cBot systems. Download and review the release notes for details about this release.

bcl2fastq2 Conversion Software v2.19

This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2.19, 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 v2.19 can be used to convert BCL files from all Illumina sequencing systems running RTA version 1.18.54 and above, and replaces v2.18. 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.

Illumina Amplicon Viewer Online Help

This document describes the parts and functionality of Amplicon Viewer. Amplicon Viewer has been designed and developed for off-instrument visualization and post-alignment analysis of TruSeq Custom Amplicon (TSCA) data. Amplicon Viewer allows you to view data (including coverage, Q score, variant call score, etc.) from multiple MiSeq amplicon runs simultaneously and interactively. You may also export custom reports based on selected samples/targets/variants.

TruSeq Custom Amplicon Kit Support - Control Manifest ACP1 Download

This file contains the sequences and targeted regions corresponding to the Amplicon Control Oligo Pool 1 (ACP1) provided in the TruSeq Custom Amplicon Kit, for use in MiSeq reporter.

Local Run Manager Targeted RNA Analysis Module Installer and Release Notes

Designed for libraries prepared with the TruSeq Targeted RNA Expression kit, the Targeted RNA analysis module aligns reads specified in the manifest file, quantifies the relative expression of genes and isoforms between samples, and then compares abundance across samples.

Local Run Manager Off-Instrument Installer

Download Local Run Manager Off-Instrument if using a MiSeq. Install Local Run Manager Off-Instrument before installing the Local Run Manager RNA Fusion analysis module. 

This download contains the Local Run Manager Off-Instrument installer, release notes, and software guide.

bcl2fastq Conversion Software v1.8.4

This download contains the software, release notes, and user guide for bcl2fastq Conversion Software v1.8.4, which can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. This software requires a Linux operating system.

The bcl2fastq Conversion Software v1.8.4 software can be used to convert BCL files from MiSeq and HiSeq sequencing systems running RTA versions earlier than 1.8. The bcl2fastq Conversion Software v1.8.4 added the ability to mask multiple adapter sequences per read and configure stringency for the adapter masking feature. The software includes standard Illumina adapter sequences.

Analysis Visual Controller (AVC) v 1.7

This download contains the Installer, Installation Guide and User Guide for the Analysis Visual Controller (AVC) v1.7 software. Please unzip the AVC.zip file to access the AVC.exe installer. AVC 1.7 replaces the earlier version of AVC (AVC 1.6), as well as the older Pipeline Visual Controller (PVC) software.

GenomeStudio 2.0 Plug-ins

This download contains supported plug-ins for extending the functionality of GenomeStudio Software 2.0.

HiSeq 3000 v3.3.20 Software

The download contains the HiSeq Software Suite and includes HiSeq Control Software (HCS), Real-Time Analysis (RTA), Recipe Fragments, Sequencing Analysis Viewer (SAV), and the BaseSpace Broker. This software is for the HiSeq 3000 system. Download and review the customer release notes for details about this release.

TruSight Cancer Content Set Product Files

This manifest file contains the list of targeted regions corresponding to the TruSight Cancer Content Set. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of TruSight Cancer set.

This bed file contains information on the TruSight Cancer Content Set. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information.

Note regarding biomarker patents and other patents unique to specific uses of products.

Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents. Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application.

NextSeq System Suite v2.0

The NextSeq System Suite v2.0 is the most recent release of the NextSeq system software. The NextSeq System Suite is user-installable. This release includes updates to the NextSeq Control Software and NextSeq Service Software. Changes include support for BeadChip scanning functionality on NextSeq 550 systems only. NCS v2.0 is compatible with NextSeq 500 systems. NextSeq 500 system users will not observe any functional differences between NCS v2.0 and NCS v1.4. NCS 2.0 is not compatible with v1 reagents. Continue using NCS v1.3.2 with v1 reagents.

To install this update, download the software installed NextSeq System Suite v2.0, and copy it to the NextSeq desktop or an accessible network location. From NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. Before installing the update, first read Important Information About Updating NCS v2.0.

MiSeq Reporter v2.2.31.1 Software Installer

This installer can be used to install MiSeq Reporter v2.2.31.1 on a computer other than the MiSeqDx instrument computer for analyzing data from the MiSeqDx IVD assays.

CalculateDiversity
This download contains the program calculateDiversity, which will produce an estimate of the diversity and of the distribution of the fragment sizes for all Genome Analyzer flow cell lanes in the input directory where the export files are available for both read 1 and read 2. The program is available as a tarball that contains the executable and a short README that gives a reference to the method and a short overview of how to run the program. The estimation is based on "Genomic mapping by fingerprinting random clones: a mathematical analysis." Lander ES and Waterman MS. Genomics. 1988 Apr;2(3):231-9.

 

Sequencing Coverage Calculator

Sequencing Coverage Calculator - This calculator helps with determining the reagents and sequencing runs that are needed to arrive at the desired coverage for your experiment. 

Cluster Station Sample Sheet Editor

This download contains the installation instructions and a compressed archive file containing the sample sheet editor update for SCS 2.4 compatibility, as well as the required Microsoft .NET 3.5 Framework installer.

Local Run Manager Amplicon DS Analysis Module Installer and Release Notes

The Amplicon DS analysis module aligns reads against the reference specified in the manifest file, and then performs variant analysis. This workflow is designed specifically for dual-strand targeted resequencing assays.

Enrichment Analysis Workflow for Nextera Rapid Capture data

This demo dataset has been provided, by Illumina, so that users can validate the installation of the Enrichment workflow within the HiSeq Analysis Software (HAS). The data folder (NexteraRapidCapture_DemoData) contains a Run Folder and a README.txt. Briefly, the Run Folder contains 10% of tiles from one lane of reads belonging to the Coriell Sample: GM10861 (http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM10861) enriched using the Nextera Rapid Capture Exome Kit and sequenced as a 12plx run. Details on running HAS, expected run time, input and output files can be found in the README.txt. The tar.gz folder can be unzipped using the following command: $tar -zxvf NexteraRapidCapture_DemoData

TruSight RNA Fusion Panel Gene List

This download contains the gene list (.txt and .xlsx) for the TruSight RNA Fusion Panel.

Local Run Manager Resequencing Analysis Module Installer and Release Notes

Intended for whole-genome sequencing of small genomes, the Resequencing analysis module aligns reads against the specified reference, and then performs variant analysis.

HCS 2.0.12 Software for HiSeq 2500, 2000, 1500, and 1000 Systems

This download contains an update to the HiSeq Control Software (HCS), Real-Time Analysis (RTA) software, Sequencing Analysis Viewing (SAV), and BaseSpace broker software.

Recommended for all HiSeq systems (not compatible with HiScan SQ systems at this time).

ATTENTION: Software installation on HiSeq 1000 and HiSeq 2000 systems when upgrading from HCS 1.5.15.1 or earlier versions must be completed by an Illumina Support representative. Please contact Illumina Technical Support or your Illumina FAS for assistance with the software upgrade. You can install the software without assistance on HiSeq 1500 and HiSeq 2500 systems.

Nextera Rapid Capture Expanded Exome Product Files

This download contains the Nextera Rapid Capture Expanded Exome targeted regions manifest files (.txt and .bed), and the exome probe manifest. The targeted regions manifest files list the 201,071 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19. The expanded exome probe manifest file lists the 347,517 enrichment probes with chromosome location in GRCh37/hg19.

The Nextera Rapid Capture Expanded Exome Targeted Regions Manifest and the Nextera Rapid Capture Expanded Exome Probe Manifest files are in .txt format. This format is required by the HiSeq Analysis Software.

 

NextSeq System Suite v2.0.2

The NextSeq System Suite v2.0.2 is the most recent release of the NextSeq system software. The NextSeq System Suite is user-installable. This release includes updates to the NextSeq Control Software and Real-Time Analysis (RTA2) software. Changes include an update for BeadChip part numbers on NextSeq 550 systems only. RTA2 has been updated to improve demultiplexing performance for low-plexity samples. NCS 2.0.2 is not compatible with v1 reagents. Continue using NCS v1.3.2 with v1 reagents.

To install this update, download the software installed NextSeq System Suite v2.0.2, and copy it to the NextSeq desktop or an accessible network location. From NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update.

Universal Kit 1.0 Manifest File Template

Template to assist with the creation of the manifest file that contains information about targeted genomic regions. This is required for MiSeq Reporter to run the Universal Kit 1.0 analysis.

BlueFuse Workflow Manager Download

Use the BlueFuse Workflow Manager link to access the website where you can download the BlueFuse Workflow Manager installer from the customer log in area.

TruSight Inherited Disease Content Set Product Files

This manifest file contains the list of targeted regions corresponding to the TruSight Inherited Disease Content Set. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of TruSight Inherited Disease set.

This bed file contains information on the TruSight Inherited Disease Content Set. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information.

Note regarding biomarker patents and other patents unique to specific uses of products.

Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents. Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application.

TruSeq Exome Library Prep Kit Product Files

Probes manifest file (.txt) and targeted region manifest files (.txt, .bed) for the TruSeq Exome Library Prep Kits.

NextSeq System Suite v1.3.2

The NextSeq System Suite v1.3.2 is user-installable. This release includes updates to the NextSeq Control Software, RTA2, NextSeq Service Software, NextSeq recipes, and the BaseSpace Broker. Changes include a reduction in template loading volume and a flow cell recovery workflow. Version 1.3.2 is compatible with v1 reagents, streamlines system shutdown and restart procedures, and adds indications for software update and wash notifications.

To install this update, download the software installer NextSeq System Suite v1.3.2, and copy it to the NextSeq desktop or an accessible network location. From the NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. Before installing the update, first read Important Information About Updating Your Software.

HiSeq Analysis Software v0.9

This download contains the source files, scripts, and documentation necessary for installing and running the HiSeq Analysis Software, Version 0.9, on a Linux operating system. The changes are recorded in the Release Notes available in the documentation.

Cluster Station Recipe Update Installer

This download contains the combined installer for Cluster Generation Kits v2 and v4. This installer contains both v5.x and v7.x recipes for use with Cluster Generation Kits v2 and v4 respectively.

GenomeStudio 2.0.2

This download includes the installers and Release Notes for GenomeStudio Software 2.0.2, which includes the Genotyping v2.0.2 and Polyploid Genotyping v2.0.2 modules. To run the Methylation and Gene Expression modules, continue running GenomeStudio Software 2011.1, which can be installed side-by-side with GenomeStudio Software 2.0.2.

Nextera Rapid Capture Exome Targeted Regions Manifest v1.2 ReadMe

This document describes the changes introduced in the Nextera Rapid Capture Exome v1.2 manifest files.

TruSeq Rapid Exome Library Prep Kit Product Files

Probes manifest file (.txt) and targeted region manifest files (.txt, .bed) for the TruSeq Rapid Exome Library Prep Kits.

Local Run Manager Amplicon Analysis Module Installer and Release Notes

The Amplicon analysis module aligns reads against the reference specified in the manifest file, and then performs variant analysis.

NextSeq System Suite v1.4

The NextSeq System Suite v1.4 is user-installable. This release includes updates to the NextSeq Control Software, RTA2, NextSeq Service Software, NextSeq recipes, and the BaseSpace Broker. Changes include support for v2 reagent kits. Version 1.4 enables BaseSpace run monitoring, reagent purging, and an updated RTA quality model (Q-table) for generating Q-scores for v2 reagents. NCS v1.4 is not compatible with v1 reagents. Continue using NCS v1.3.2 with v1 reagents.

To install this update, download the software installer NextSeq System Suite v1.4, and copy it to the NextSeq desktop or an accessible network location. From the NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. Before installing the update, first read Important Information About Updating Your Software.

MiSeq Software Updater

For details about MiSeq Software Updater v2.6, see the MiSeq Software v2.6 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 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.

HCS 2.2.58 Software for HiSeq 2500, 2000, 1500, and 1000 Systems

The download contains an update to the HiSeq Software Suite and includes new versions of HiSeq Control Software (HCS), Real-Time Analysis (RTA), Recipe Fragments, Sequencing Analysis Viewer (SAV), and the BaseSpace Broker. This software includes support for Rapid Run mode using HiSeq Rapid v2 chemistry and an update to the maintenance wash to support only maintenance wash solution (Tween 20 and ProClin 300) protocol. This software is for all HiSeq systems except HiSeq X and HiScanSQ. Download and review the customer release notes for details about this release.

TruSight One Sequencing Panel Manifest File Download

This manifest file contains the list of targeted regions corresponding to the TruSight One Sequencing Panel. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of the TruSight One Sequencing Panel.

This bed file contains information on the TruSight One Sequencing Panel. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information.

Note regarding biomarker patents and other patents unique to specific uses of products.

Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents. Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer's specific application.

cBot Software v3.0.56 Installer

This download contains the installer for cBot software v3.0.56, which includes HiSeq3000/4000 SR and PE custom primer recipes. This software is compatible with both cBot and cBot2 instruments.  

cBot Software v2.0.29 Installer

This download contains the installer for cBot software v2.0.29, which includes recipes required for the HiSeq v2 rapid flow cell and HiSeq X HD v2 reagent kit with a HiSeq X flow cell.

Local Run Manager DNA Enrichment Analysis Module Installer and Release Notes

The DNA Enrichment analysis module aligns reads against the whole genome reference, and then performs variant analysis for regions of interest specified in the manifest file.

cBot Software v2.0.34 Installer

This download contains the installer for cBot software v2.0.34, which includes recipes required for the HiSeq 3000/4000 Cluster Kit with a HiSeq 3000/4000 flow cell.

Nextera Rapid Capture Expanded Exome Unique Intervals File

"This download contains the Nextera Rapid Capture Expanded Exome target region intervals that do not overlap the Nextera Rapid Capture Exome target regions. There are a total of 29 MB that are unique to the Expanded Exome product. 50,257 intervals across 47,273 Expanded Exome targeted regions. This was determined by base overlap only. For example, comparing an Exome product region at Chr 1 position 300 – 500 with an Expanded Exome region at Chr 1 position 305 – 495 results in a 191 bp overlap and two 5 bp ""unique regions"" for the Exome product."

Local Run Manager Generate FASTQ Analysis Module Installer and Release Notes

The Generate FASTQ analysis module demultiplexes indexed reads, generates intermediate analysis files in the FASTQ file format, and then exits the workflow. FASTQ files are input for third-party analysis tools.

NextSeq System Suite v2.1.2

The NextSeq System Suite v2.1.2 is the most recent release of the NextSeq system software. The NextSeq System Suite is user-installable. This release includes updates to the NextSeq Control Software and Real-Time Analysis (RTA) software. 

To install this update, download the software installed NextSeq System Suite v2.1.2, and copy it to the NextSeq desktop or an accessible network location. From NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update.

Local Run Manager Software Release Notes

This download contains the release notes for Local Run Manager software.

Sequencing Analysis Viewer v1.8.37 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from HiSeq 1000/2000, Hiseq 1500/2500, MiSeqs (with MiSeq Control Software v2.5 and lower), Genome Analyzer IIx, and HiScanSQ. Download and unzip this file to install SAV 1.8 to view sequencing runs on an offline computer. Also available are the release notes and the user guide.

HiSeq 4000 v3.3.20 Software

The download contains the HiSeq Software Suite and includes HiSeq Control Software (HCS), Real-Time Analysis (RTA), Recipe Fragments, Sequencing Analysis Viewer (SAV), and the BaseSpace Broker. This software is for the HiSeq 4000 system. Download and review the customer release notes for details about this release.

cBot Software v2.0.16 Installer

This download contains the installer for cBot software v2.0.16, which includes recipes required for HiSeq v4 high output chemistry and flow cells and HiSeq X HD chemistry and flow cells. For additional details, see the release notes and installation notes before installation.

Genome Analyzer SCS 2.10/RTA 1.13 and SAV 1.8 Software

This download contains an update to the Genome Analyzer’s Sequencing Control Software (SCS) and Real-Time Analysis software (RTA). This release enables dual indexing with Illumina Nextera sample prep on Genome Analyzer (GA) systems. SCS2.10/RTA1.13 should be installed solely on your GA PC (running SCS2.9 and lower) and is user installable. An individual download of the Sequncing Analysis Viewer (SAV) software version 1.8 is also provided as a separate download. Note that SCS 2.10/RTA 1.13 requires the use of OLB 1.9.4 to perform offline base calling if necessary. SCS2.9/RTA1.9 data requires the use of OLB1.9.3. Critical documents to review before installation of the new software are provided as links below: 1) Technical note with background on the changes, the benefits provided and considerations prior to upgrading. 2) Release Notes and Install Notes; this is the first SCS/RTA update where the SCS and RTA Software installers need to be run separately. 3) SCS2.0/RTA1.9 software can still be used for “single indexing”. For instructions on the creation of a SCS2.9/RTA1.9 icon side by side with the SCS2.10/RTA1.13 one, review “SCS2 9_Icon_Instructions”.

Illumina User Management v1.0.0.6 Software Installer

This installer can be used to install the Illumina User Management software (v1.0.0.6) to create a user database file for use with the MiSeqDx system. This user database file controls user passwords and privileges for the MiSeqDx Operating Software.

NeoPrep System Suite v1.1.2

The NeoPrep System Suite v1.1.2 is an update of the NeoPrep Library Prep System software and enables quantification and normalization on the TruSeq Stranded mRNA protocol. The NeoPrep System Suite is user-installable. This release includes the NeoPrep Control Software 1.1, NeoPrep Protocols v1.1.2, and BaseSpace Broker 2.7.0.30.

GenomeStudio Polyploid Clustering Module v1.0 Software

This download include the installer and Release Notes for the GenomeStudio Polyploid Clustering Module v1.0. This module is a standalone installation, however, Illumina recommends to install the GenomeStudio v2011.1 framework and Genotyping Module as a prerequisite prior to installing the Polyploid Clustering Module. The Polyploid Clustering Module can be used for automated cluster analysis of polyploid genomes. The module intentionally does not call genotypes. Instead, it allows the user to factor in experimental design and sample biology and combine the population level cluster analysis to intelligently call genotypes in a workflow outside of GenomeStudio.

TruSight Cardiomyopathy Content Set Product Files

This manifest file contains the list of targeted regions corresponding to the TruSight Cardiomyopathy Content Set. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of TruSight Cardiomyopathy set.

This bed file contains information on the TruSight Cardiomyopathy Content Set. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information.

Note regarding biomarker patents and other patents unique to specific uses of products.

Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents. Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application.

Illumina no longer accepts orders for TruSight Cardiomyopathy. The recommended replacement product is the TruSight Cardio Sequencing Kit. Illumina remains committed to providing you with high-quality support and service.

TruSeq Amplicon Support - Cancer Panel Manifest File Download

TruSeq Amplicon - Cancer Panel Manifest File (.txt)

Local Run Manager TruSight Tumor 15 Analysis Module Installer and Release Notes

Designed for libraries prepared with the TruSight Tumor 15 kit, the TruSight Tumor 15 analysis module aligns reads specified in the manifest file, and then reports somatic variants of a set of reference panel genes associated with cancer.

Universal Kit 1.0 Manifest File Instructions

Instructions to assist with the creation of the manifest file which is required for MiSeq Reporter to run the Universal Kit 1.0 analysis.

Genome Analyzer SCS 2.9/RTA 1.9 and SAV 1.7 Software

This download contains an update to the Genome Analyzer�s sequencing control and real-time analysis software (SCS2.9/RTA1.9). This update enables control processing and reporting for TruSeq sample prep controls as well as important bug fixes and stability enhancements. SCS2.9/RTA1.9 should be installed solely on your GA PC and is user installable. Please note that SCS 2.9/RTA 1.9 requires the use of the bcl converter included in OLB 1.9.3 if processing data for analysis using CASAVA 1.7. For additional details about this software update, please review the Release Notes and Install Notes for SCS 2.9/RTA 1.9 (available for individual download as .pdf files below) before installing.

TruSight Exome Content Set Product Files

This manifest file contains the list of targeted regions corresponding to the TruSight Exome Content Set. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of TruSight Exome set.

This bed file contains information on the TruSight Exome Content Set. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information.

Note regarding biomarker patents and other patents unique to specific uses of products.

Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents. Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application.

Polyploid Genotyping Module Demo Dataset - Potato

This download contains the Polyploid Genotyping Module Demo Dataset - Potato.

Local Run Manager Small RNA Analysis Module Installer and Release Notes

Designed for libraries prepared with the TruSeq Small RNA kit, the Small RNA analysis module aligns reads against databases for contaminants, mature miRNA, small RNA, and a genomic reference, and then measures abundance of short RNA sequences.

TruSight RNA Fusion Target Regions File

This download contains target region files (.gtf and .bed) for the TruSight RNA Fusion Panel. These files are viewable in IGV or UCSC.

GenomeStudio Software 2011.1

This download includes the installers, README, and Release Notes for GenomeStudio dbSNP129 and dbSNP130, the GenomeStudio Software 2011.1 Framework, and the following GenomeStudio Modules: Genotyping v1.9, Gene Expression v1.9, and Methylation v1.9. 

To run the Genotyping module, users are encouraged to install and run GenomeStudio Software 2.0.

License keys for each GenomeStudio module are included in a text file with the software download.

Nextera Rapid Capture Exome vs. Expanded Exome Overlap File

"This download contains the Nextera Rapid Capture Exome targeted region intervals that overlap the Nextera Rapid Capture Expanded Exome targeted regions. The total overlap is 33.0 MB between the two products. 189,522 overlapping intervals across 188,621 Exome targeted regions. This was determined by base overlap only. For example, comparing an Exome product region at Chr 1 position 300 – 500 with an Expanded Exome region at Chr 1 position 305 – 495 results in a 191 bp overlap and two 5 bp ""unique regions"" for the Exome product."

HCS 1.5.15.1/RTA 1.13/SAV 1.8 Software

This download contains an update to the HiSeq Control Software (HCS), Real-Time Analysis (RTA) Software and Sequencing Analysis Viewing (SAV) Software for the HiSeq and HiScan SQ systems. It is recommended for any system running HCS1.5.15.0 or HCS1.4.8 and lower. For HCS1.4.8 7 users, the release updates recipes and configurations required for use when sequencing Nextera prepared libraries. For HCS1.5.15.0 users, this release fixes a memory leak causing crashes as the first Flow Cell completes. It also reduces the memory footprint of RTA to help mitigate some errors that have been occurring due to communication dropouts (the Flow Cell layout now has 16 tiles per swath instead of 8).

cBot Software v3.0.40

This document describes the changes and features introduced in cBot software v3.0.40, which includes support for internal barcode scanning on cBot 2. This software is for the cBot 2. Download and review the release notes for details about this release.

To install this software, contact your Illumina field representative.

HCS 2.2.38 Software for HiSeq 2500, 2000, 1500, and 1000 Systems

This download contains an update to the HiSeq Software Suite and includes new versions of HiSeq Control Software (HCS), Real-Time Analysis (RTA), Recipe Fragments, Sequencing Analysis Viewer (SAV), and the BaseSpace Broker. This software is for all HiSeq systems except HiSeq X and HiScanSQ. Download and review the customer release notes for details about this release. This package is customer installable, but review the installation notes to make sure that your system meets the requirements for this update.

GenomeStudio Software 2009.2

This download includes the installers, README, and Release Notes for GenomeStudio 2009.2 Framework.

Local Run Manager RNA Fusion Analysis Module, RNA Fusion Reference Genome, and Release Notes

The Local Run Manager RNA Fusion analysis module aligns reads against a specified reference and detects gene fusions. This module is designed specifically for RNA libraries prepared with the TruSight RNA Fusion Panel kit. 

This download contains the module installer, RNA Fusion reference genome, and release notes.

TruSight Myeloid Product Files

These manifest files contain the list of targeted regions and sequences corresponding to the TruSight Oligos (TSO) provided in the TruSight Myeloid Sequencing Panel kit. MiSeq Reporter Software uses these files for the analysis of the TruSight DNA Amplicon set.

HiSeq Analysis Software hg19 Reference Genome

This download contains the human reference genome hg19 from UCSC for the HiSeq Analysis Software (tar).

TruSeq RNA and DNA v2 Kits Support - Controls Download

The TruSeq RNA and DNA v2 kits include adapters for 12 new indexes. RTA versions 1.12 and earlier cannot recognize these indexes and assign control reads from these indexes. To resolve this issue, replace the controls.fasta file on the instrument PC with this new version. This is only necessary for customers who are using TruSeq v2 DNA or RNA kits and sample prep controls. If customers are not using sample prep controls, RTA does not need to identify indexes. In this case, replacing the controls.fasta file is not necessary. Sample demultiplexing happens after RTA analysis and is not affected by this issue.

TruSight Tumor 26 Product Files

These manifest files contain the list of targeted regions corresponding to the TruSight Tumor 26 Content Set. These files are used by Illumina Experiment Manager (v1.6 or greater) and MiSeq Reporter Software (v2.2 or greater) for the analysis of TruSight Tumor 26 set.

Nextera Rapid Capture Exome v1.2 Product Files

This download contains the Nextera Rapid Capture Exome v1.2 release notes, targeted regions manifest files (.txt and .bed), and the exome probe manifest. The readme document describes the Nextera Rapid Capture Exome v1.2 manifest files. The targeted regions manifest files list the 214,126 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.

The Nextera Rapid Capture Exome v1.2 Targeted Regions Manifest and the Nextera Rapid Capture Exome Probe Manifest files are in .txt format. This format is required by the HiSeq Analysis Software.