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.

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Description
 
File Info
Date
Human660W-Quad v1.0 Product Support Files

This set of files includes the product support files the 660W-Quad including: GenomeStudio demo workspace, minor allele frequencies, physical and genetic coordinates, gene annotation files, build 36 -> build 37 mapping information, demo sample sheet, gentrain sample sheet and simple marker list. All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

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.

HumanKaryomap-12 v1.0 BeadChip Product Files

Manifest (.bpm) and cluster file (.egt) for the HumanKaryomap-12 v1.0 BeadChip.

HumanHT-12 v3 binary manifest file (.txt)

This download contains a binary manifest file in text format for the HumanHT-12 v3 Gene Expression BeadChip. Annotation updated March 2010

Mouse MD Linkage Product Files

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Mouse MD Linkage Panel.

GeneSeek GGP Porcine LD Product Files

This download contains the manifest files in BPM and CSV format, the cluster file, and the strand report for the GeneSeek GGP Porcine LD array.

HumanExome-12 v1.2 Support Files

This download contains support files for the HumanExome-12 v1.2 BeadChip.

RatRef-12 v1.0 Manifest Files

This download contains binary manifest files in *.txt and *.bgx format for the RatRef-12 v1.0 Gene Expression BeadChip. 

 

HumanOmni2.5Exome-8 v1.1 Product Files

Product files for the Infinium HumanOmni2.5Exome-8 v1.1 BeadChip. These files include the Cluster File (.egt), Manifest File (.bpm and .csv) and LIMS Product Descriptor (.xml).

GoldenGate Methylation Cancer Panel Product Files

This download contains: a document describing the gene content, a gene annotation file, a CpG file, and the manifest (.oma) for the GoldenGate Methylation Cancer Panel I.

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."

HumanOmniExpress-24 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmniExpress-24 v1.0 BeadChip.

Beeline Software v2.0

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

Humancvd v1.0 Product Files

This download contains the Manifest (.bpm) and Cluster File (.egt) for the HumanCVD v1.0 DNA Analysis BeadChip.

BeadScan Software Addendum Version 3.0 (11206805)

Instructions for using the BeadScan Software.

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.

OncoArray-500K v1.0 Support Files

This download contains the latest genotype reports, minor allele frequencies, gene annotation file, demo data, locus report, reproducibility and heritability report, population report, and sample sheets for the OncoArray-500K v1.0 BeadChip.

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.
HumanHT-12 v3.0 Gene Expression BeadChip Product Files

This download contains the manifest files (.bgx and .txt) for the HumanHT-12 v3.0 Gene Expression BeadChip. These manifest files can be used with any version of BeadStudio.

BlueFuse Multi Software Download

Use the BlueFuse Multi Software Installer link to access the website where you can download the BlueFuse Multi Software installer from the customer log in area.

Infinium HD Methylation SNP List

A list of SNPs that could potentially impact methylation array results if present in the test population.

GeneSeek GGP Bovine 150K Product Files

This download contains the manifest files in BPM and CSV format, and the cluster file for the GeneSeek GGP Bovine 150K array.

Infinium BovineLD v1.0 BeadChip Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), markerlist (.txt), and LIMS Product Descriptor File (.xml) for the BovineLD v1.0 DNA Analysis BeadChip.

HumanMethylation450K v1.0 Content Descriptor File

Content descriptor file for the HumanMethylation450K chip which is required for Accession Methylation BeadChips into LIMS.

GoldenGate Linkage V Product Files

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the GoldenGate Linkage V Panel Set.

Infinium Omni2.5Exome-8 v1.2 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Infinium Omni2.5Exome-8 v1.2 BeadChip.

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.

HumanOmni5Exome-4 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmni5Exome-4 v1.1 BeadChip.

Sequencing Analysis Viewer v1.11 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiniSeq, MiSeq, 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, continue using SAV 1.8.37.

BovineHD Product Files

This download contains the Manifest (.bpm), Cluster file (.egt), and LIMS Product Descriptor (.xml) for the BovineHD DNA Analysis BeadChip. Infinium LIMS users, please note the Product Descriptor file (.xml) is REQUIRED FOR PROCESSING this BeadChip.

Infinium OmniExpressExome-8 v1.4 Product Files

This download contains the manifest, cluster, and product descriptor files for the Infinium OmniExpressExome-8 v1.4 BeadChip. Use the manifest file appropriate for the reference genome you are using.

Infinium Omni5-4 v1.1 Support Files

This downloads page includes product support files for the Infinium Omni5-4 v1.1 Kit.

Infinium QC Array-24 v1.0 Support Files

This download contains a file for UCSC browser (.bed), gene annotation file (.txt), demo data (.zip), sample sheet demo (.csv), reproducibility and heritability report (.csv), loci name to rsID conversion file (.txt), strand report (.txt), mapping comments file (.txt), physical and genetic coordinates file (.txt), population reports (.zip), legacy overlap file (.txt), missing legacy SNPs file (.txt), additional SNPs file (.txt), and prior product modification file (.txt) for the Infinium QC Array-24 Kit.

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.

HumanOmniExpress-12 v1.0 Support Files
These files contain the cluster files, beadpool manifest, gentrain reports, and sample sheet for the OmniExpress v1.1 product release
Illumina Experiment Manager v1.11

The Illumina Experiment Manager v1.11 is a desktop tool that guides you in building library plates and creating the sample sheet used with the MiSeq, NextSeq, HiSeq and NeoPrep systems.

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.

Mouse LD Linkage Product Files

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Mouse LD Linkage Panel.

Infinium BovineLD BeadChip Workspace

This download contains the complete workspace for the BovineLD DNA Analysis BeadChip

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.

HumanOmniZhongHua-8 v1.1 Support Files

This download contains the mapping comments and prior product modifications files for the HumanOmniZhongHua-8 v1.1 BeadChip.

Infinium Core-24 v1.0 Support Files

This download contains support files for the Infinium Core-24 v1.0 Kit.

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.

HumanOmni5Exome-4 v1.0 Support Files

Support files for the Infinium HumanOmni5Exome BeadChip.

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.

HumanOmniExpressExome-8 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmniExpressExome-8 v1.0 BeadChip.

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.

Infinium CoreExome-24 v1.1 Support Files

This download contains product support files for the Infinium CoreExome-24 v1.1 BeadChip.

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.

HumanOmniExpress-24 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster (.egt), and LIMS product descriptor files for the HumanOmniExpress-24 v1.1 BeadChip.

Note: To download BPM files, hover over the link, right-click, and select "Save target as...".

HumanOmni2.5-8 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmni2.5-8 v1.0.

Human Linkage V Panel Product Files

This download contains the Manifests (.opa), BeadStudio Project (.bsc), and annotation files for the GoldenGate Human Linkage V Panel.

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.

OncoArray-500K v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the Infinium OncoArray-500K v1.0 BeadChip Kit.

Infinium MethylationEPIC Product Files

Manifest file (.bpm and .csv), manifest column headings descriptor file (.pdf), and content descriptor file (.xml), additional SNPs (.xml), and missing legacy SNPs (.xml) for the Infinium MethylationEPIC BeadChip.

iControlDB Product Template Files
Generic BeadChip-specific case reports which can be used if no case reports are available.
HumanOmni1S-8 v1.0 Product Support Files

This set of files includes the product support files the Omni1S-8 v1.0 including: GenomeStudio demo workspace, minor allele frequencies, physical and genetic coordinates, gene annotation files, simple marker list, build 36 -> build 37 mapping files, demo sample sheet, gentrain sample sheet and markers-of-interest file. These support files are the same for the sinlge-use and multi-use versions of the Omni1S-8. All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

HumanLinkage-24 Product Files

This download contains the Manifest (.bpm) and product descriptor file (.xml) for the HumanLinkage-24 BeadChip. Please note that this was originally a custom iSelect panel that has been made available to the public. Therefore not cluster file or supporting files are available.

GoldenGate ImportManualBatch MUN Template (15004541 A)

This download contains a comma-separated values file to use as a template for the Illumina LIMS Import Manual Batch function to create a customized batch of DNA samples with MUN plates from a single GoldenGate Assay project.

Infinium CoreExome-24 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Infinium CoreExome-24 v1.1 BeadChip. Use the manifest file appropriate for the reference genome you are using.

Sequencing Analysis Viewer v1.9.1 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiSeq, NextSeq, HiScanSQ, HiSeq X, and all HiSeq systems. Download and unzip this file to install SAV for viewing sequencing runs on an offline computer. Changes associated with this version of the software are included in the software release notes. This SAV version requires Windows .NET Framework 4.5. If your system is using Windows .NET Framework 4, continue using SAV 1.8.37.

Infinium Omni5-4 v1.2 Product Files

This downloads page contains the latest manifest files in BPM and CSV formats, the LIMS product descriptor file, and the cluster file for the Infinium Omni5-4 v1.2 Kit. Use the manifest file appropriate for the reference genome you are using.

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.

Infinium BovineLD BeadChip allele report

This download contains the allele report for the BovineLD DNA Analysis BeadChip.

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.

 

Ship Schedule Change Form

Shipping schedule change request form.

HumanCytoSNP-12 v2.1 Product Support Files

This set of files includes the product support files the CytoSNP-12 v2.1 including: GenomeStudio demo workspace, minor allele frequencies, physical and genetic coordinates, gene annotation files, simple marker list, markers-of-interest file, build 36 to build 37 mapping information, and sample sheets for the demo workspace and gentrain data (iControlDB). All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

HumanMethylation27 Product Support Files

This download contains the content list (.xlsx) for the HumanMethylation27 BeadChip.

HumanCoreExome-24 v1.0 Support Files

This download contains a sample sheet demo (.csv), reproducibility and heritability report, rsIDs (.txt), for the HumanCoreExome-24 v1.0 BeadChip Kit.

VeraReport Software v1.0.6.3

This download contains the VeraReport installer and documentation, enabling you to install the VeraReport software on other computers besides the instrument workstation.

HumanExome-12 v1.0 Support Files

This download contains support files for the Infinium HumanExome-12 v1.0 BeadChip.

 

Infinium ImmunoArray-24 v2.0 Support Files

This download contains a file for UCSC browser (.bed), gene annotation file (.txt), locus report (.txt), demo data (.zip), sample sheet demo (.csv), reproducibility and heritability report (.csv), loci name to rsID conversion file (.txt), strand report (.txt), mapping comments file (.txt), population reports (.zip), prior product modification file (.txt), legacy overlap file (.txt), missing legacy SNPs file (.txt), and additional SNPs file (.txt) for the Infinium ImmunoArray-24 v2.0 BeadChip.

GoldenGate ImportManualBatch SUD Template (15004542 A)

This download contains a comma-separated values file to use as a template for the Illumina LIMS Import Manual Batch function to create a customized batch of DNA samples with SUD plates from a single GoldenGate Assay project.

Cardio-MetaboChip Product Files

This download contains the manifest file (.bpm), cluster file (.egt) and product descriptor file (.xml) for the Cardio-MetaboChip.

HumanOmni1S-8 v1.0 Multi-Use Product Files

This download contains the manifest files (.bpm and .csv), cluster file (.egt) and product descriptor file (.xml) for the HumanOmni1S-8 v1.0 Multi-Use DNA Analysis BeadChip.

Sequencing Analysis Viewer v1.10.2 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiSeq, NextSeq, HiScanSQ, HiSeq X, and all HiSeq systems. Download and unzip this file to install SAV for viewing sequencing runs on an offline computer. For changes associated with this version of the software, see the HiSeq X Instrument Software Release Notes (15056499 D). This SAV version requires Windows .NET Framework 4.5.1. If your system is using Windows .NET Framework 4, continue using SAV 1.8.37.

PorcineSNP60 v2.0 Support Files

This download contains the mapping comment file (.txt) and annotation file (.csv) for the PorcineSNP60 v2.0 BeadChip.

MaizeSNP50 v1.0 Product Files

This download contains the Manifest (.bpm and .csv) and Cluster File (.egt) for the MaizeSNP50 v1.0 DNA Analysis BeadChip. Infinium LIMS users, please note the Product Descriptor file (.xml) is REQUIRED FOR PROCESSING this BeadChip. *Update* The MaizeSNP50 cluster file has been updated. Working together with TraitGenetics, one of the core content contributors for this consortium-driven product, genotype calling accuracy has been improved with the removal or editing of loci that exhibited a combination of two or more heritability or reproducibility errors. Furthermore, loci with two or more parental lines represented in the heterozygous cluster have been excluded. This evaluation, with a deeper look at heritability across numerous trios, identified markers to edit or remove and improves the overall accuracy of the cluster positions. Please note that it is expected to have some variation across genotyping sites, so each project does require some evaluation analysis. Illumina recommends always including a small number of trios and replicates in each project to help identify loci that may require editing.

HumanOmniExpressExome-8 v1.2 Support Files

This download contains the reproducibility and heritability report, the minor allele frequencies file, the demo sample sheet, the gene annotation file, the loci name to rsID conversion file, the prior product modifications file, and the mapping comments file for the HumanOmniExpressExome-8 v1.2 BeadChip.

RatRef-12 v1.0 Product Files

This download contains a binary manifest file for the RatRef-12 v1 Gene Expression BeadChip. This manifest file can be used with any version of BeadStudio.

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. 

iControlDB Upload User Guide (11297381)
Instructions for uploading data to iControlDB using a phenotype information file.
Infinium Omni5Exome-4 v1.3 Support Files

This download contains product support files for the Infinium Omni5Exome-4 v1.3 Kit.

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

CytoSNP-850K BeadChip Product Files for the iScan System

Manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the CytoSNP-850K BeadChip compatible with the iScan System.

MaizeLD and MaizeLD+ v1.0 Product Files

This download contains the manifest files in BPM and CSV format for the MaizeLD and MaizeLD+ BeadChip Kit.

HumanOmniExpress-12 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmniExpress-12 v1.1 BeadChip.

GenomeStudio 2011.1 Plug-ins

This download contains supported plug-ins for extending the functionality of GenomeStudio 2011.1.

BCD Manifest File

The sample manifest file is an template example which is used to accession samples into LIMS for processing Infinium HumanMethylation450K and Infinium MethylationEPIC BeadChips.

Infinium Omni2.5Exome-8 v1.2 Support Files

This download contains a file for UCSC browser (.bed), gene annotation file (.txt), demo data (.zip), sample sheet demo (.csv), reproducibility and heritability report (.csv), loci name to rsID conversion file (.txt), strand report (.txt), mapping comments file (.txt), population reports (.zip), legacy overlap file (.txt), missing legacy SNPs file (.txt), and additional SNPs file (.txt) for the Infinium Omni2.5Exome-8 v1.2 BeadChip.

TruSight RNA Fusion Panel Gene List

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

Infinium OmniExpress-24 v1.2 Product Files

This download contains the latest manifest (.bpm and .csv), cluster (.egt), and LIMS product descriptor files for the Infinium OmniExpress v1.2 BeadChip. Use the manifest file appropriate for the reference genome you are using.

HumanOmniZhongHua-8 v1.2 Support Files

This download contains the latest sample sheet, demo sample sheet, strand report, reproducibility and heritability report, mapping comments, loci report, rsID, and gene annotation files for the HumanOmni2.5-8 v1.2 BeadChip.

Human660W-Quad v1.0 Product Files

This download contains the Manifest (.bpm and .csv), cluster file (.egt) and product descriptor file (.xml) for the Human660W-Quad v1.0 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

HumanCoreExome-12 v1.0 Support Files

This download contains the latest annotation file (.zip) for the HumanCoreExome-12 v1.0 BeadChip.

GoldenGate Genotyping Assay Sample Sheet Template (15006112 A)

This download contains a comma-separated values file to use as a sample sheet template for the GoldenGate Genotyping Assay.

PorcineSNP60-v1.0

This download contains the Manifest (.csv and .bpm), Cluster File (.egt) and Product Descriptor File (.xml) for the PorcineSNP60 v1.0 DNA Analysis BeadChip.

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.

HumanExome-12 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml), for the HumanExome v1.1 BeadChip.

HumanOmni5-Quad v1.0 Support Files

This set of files includes the product support files for the Omni5-Quad including: GenomeStudio demo workspace, minor allele frequencies, .bed file, gene annotation files and markers that changed from the previous manifest. All files herein are in build 37 coordinates.

HumanCytoSNP-12 BeadChip Product Files for the NextSeq 550 System

Manifest file (*.bpm) and cluster file (*.egt) for the HumanCytoSNP-12 BeadChip compatible with the NextSeq 550 system.

BeadArray Controls Reporter Installer

The BeadArray Controls Reporter software is designed to analyze the sample controls for Infinium MethylationEPIC arrays. For more information, see the BeadArray Controls Reporter Software Guide.

HumanCore-12 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml),  mapping comments, prior product modifications, and auxilliary files for the HumanCore-12 v1.0 BeadChip.

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.

HumanOmniZhongHua-8 v1.1 Product Files

This download contains the manifest files in BPM and CSV format, the cluster file, and the LIMS product descriptor file for the HumanOmniZhongHua-8 v1.1 BeadChip.

Infinium Omni2.5Exome-8 v1.3 Support Files

This download contains product support files for the Infinium Omni2.5Exome-8 v1.3 BeadChip.

HumanOmniExpress-24 v1.1 Support Files

This download contains the demo data set, population reports, demo sample sheet, gene annotation file, locus report, mapping comments file, strand report, reproducibility and heritability report, loci name to rsID conversion file, and the LIMS product descriptor file for the HumanOmniExpress-24 v1.1 BeadChip.

Infinium Omni5Exome-4 v1.2 Product Files

This download contains the latest manifest files (.bpm and .csv), cluster file, and LIMS product descriptor (.xml) file for the Infinium Omni5Exome-4 Kit.

Infinium OmniExpressExome-8 v1.3 Support Files

This download contains the reproducibility and heritability report, the minor allele frequencies file, the demo sample sheet, the gene annotation file, the loci name to rsID conversion file, the prior product modifications file, and the mapping comments file for the Infinium OmniExpressExome-8 v1.3 BeadChip.

HumanImmuno BeadChip Kit Product Files

This download contains the manifest (.bpm), cluster file (.egt) and product descriptor file (.xml) for the HumanImmuno BeadChip.

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.

 

HumanCoreExome-12 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxilliary files for the HumanCoreExome-12 v1.1 BeadChip.

HumanOmniExpress-12 v1.0 FFPE Product Support Files

This download contains the HumanOmniExpress-12 v1.0 FFPE .bed file.

HumanCytoSNP-12 v2.0 Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanCytoSNP-12 v2.0 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

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.

ADME Plug-in Setup v1.0.1.4

This download contains the ADME Plug-in Setup v1.0.1.4 installer.

Infinium Exome-24 v1.0 Support Files

This download contains product support files for the Infinium Exome-24 Kit.

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.

MHC Panel Product Files

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the MHC Panel.

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.

HumanOmni1-Quad v1.0 Multi-Use Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), and LIMS Product Descriptor (.xml) for the HumanOmni1-Quad v1.0 Multi-use DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

CanineSNP20 v1.0 Product Files

This download contains the Manifest (.bpm), Cluster File (.egt), and SNP list (.txt) for the CanineSNP20 v1.0 DNA Analysis BeadChip.

Infinium Omni2.5-8 v1.3 Support Files

This download contains the latest product support files for the Infinium Omni2.5-8 v1.3 BeadChip.

HumanOmniExpress-12 v1.0 Multi-Use Product Files

This download contains the Manifest (.bpm), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanOmniExpress-12 v1.0 Multi-use DNA Analysis BeadChip. 

WGGT Import Manual Batch Template (15004543 A)

This download contains a comma-separated values file to use as a template for the Illumina LIMS Import Manual Batch function to create a customized batch of DNA samples from a single Infinium Assay project.

HumanOmniExpressExome-8 v1.1 Support Files

This download contains the latest annotation file (.zip) for the HumanOmniExpressExome-8 v1.1 BeadChip.

Mouse MicroRNA v2.0 Assay Pool Manifest

 

This download contains a binary manifest file for the Mouse MicroRNA v2.0 Assay Pool. Use this manifest file with BeadStudio v3.0. Annotation updated Oct, 2008.

 

HumanMethylation27 Product Files

This download contains the manifest (.bpm) for the HumanMethylation27 BeadChip.

CytoSNP-850K v1.1 BeadChip Product Files for the iScan System

Manifest files (.bpm and .csv), LIMS product descriptor file (.xml), and cluster file (.egt) for the CytoSNP-850K v1.1 BeadChip compatible with the iScan System.

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.

Infinium OmniExpress-24 v1.2 Support Files

This download contains the latest manifest product support files for the Infinium OmniExpress v1.2 BeadChip.

Infinium HD Methylation Sample Sheet

This download contains a comma-separated values file to use as a sample sheet template for the Infinium HD Methylation assay.

HumanOmni2.5S-8 v1.0 Product Support Files

This link includes product support files for the Omni2.5S-8 v1.0 microarray including MAF files, Demo GenomeStudio Project, markers-of-interest file, demo sample sheet, markers of interest file, UCSC .bed file, gene annotation files, pnysican and genetic distance files, markers in ADME genes and simple marker list.

HumanOmni2.5-8 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmni2.5-8 v1.1 BeadChip.

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.

Infinium MethylationEPIC Sample Sheet

This download contains a comma-separated values file to use as a sample sheet template for the Infinium HD MethylationEPIC assay.

Infinium Methylation Assay Sample Sheet Template (11303488 A)

This download contains a comma-separated values file to use as a sample sheet template for the Infinium Methylation Assay.

GeneSeek GGP Porcine HD Product Files

This download contains the manifest files in BPM and CSV format and the cluster file for the GeneSeek GGP Porcine HD array.

Infinium Core-24 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor file (.xml) for the Infinium Core-24 v1.0 Kit. Use the manifest file appropriate for the reference genome you are using.

HumanOmni1S-8 v1.0 Product Files

This download contains the manifest files (.bpm and .csv), cluster file (.egt) and product descriptor file (.xml) for the HumanOmni1S-8 v1.0 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

Human1M-Duo v3.0 Product Files

This download contains the Manifest (.bpm and .csv), cluster file (.egt) and product descriptor file (.xml) for the Human1M-Duo v3.0 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

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.

Infinium Omni5-4 v1.2 Support Files

This downloads page includes product support files for the Infinium Omni5-4 v1.2 Kit.

HumanCoreExome-12 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanCoreExome-12 v1.0 BeadChip.

Calling Polyploid Genotypes with GenomeStudio v1.8

This download contains a technical note and instructional video describing the new polyploidy features in the GenomeStudio Genotyping Module v1.8.

Humancnv370-quad V3.0 Product Files

This download contains the Manifest (.bpm) and Cluster File (.egt) for the HumanCNV370-Quad v3.0 DNA Analysis BeadChip.

PorcineSNP60 v2.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the PorcineSNP60 v2.0 BeadChip.

HumanOmniExpress-12 v1.0 FFPE Product Files

This download contains the Manifest (.bpm), product descriptor file(.xml) and Cluster File (.egt) file for the HumanOmniExpress-12 v1.0 FFPE DNA Analysis BeadChip. These files are specific to the FFPE version of the OmniExpress BeadChip and are used for processing restored FFPE samples. Please use the normal (.bpm) and (.egt) files when processing non-FFPE samples.

HumanWG-6 Product Files

This download contains the HumanWG-6 manifest (BGX and TXT).

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.

HumanOmniExpress-12 v1.1 Support Files

This download contains the gentrain reports, sample sheet, and gene annotation files for the HumanOmniExpress v1.1 product release.

HumanOmni2.5-8 v1.0 Support Files

This set of files includes the product support files for the Omni2.5-8 v1.0 including: GenomeStudio demo workspace, minor allele frequencies, .bed file, gene annotation files and markers that changed from the previous manifest. All files herein are in build 37 coordinates.

MouseWG-6 v2.0 Gene Expression BeadChip Product Files

This download contains the manifest files (.bgx and .txt) for the MouseWG-6 v2.0 Gene Expression BeadChip. These manifest file can be used with any version of BeadStudio.

 

HumanOmniExpress-12 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), mapping comments, prior product modifications, and auxiliary files for the HumanOmniExpress-12 v1.0 product release.

HumanOmni2.5S-8v1 Multi-use Product Files

This download contains the manifest (.bpm), cluster file (.egt) and product definition file (.xml) for the Omni2.5S-8 Multi-use

GenomeStudio 2.0

This download includes the installers and Release Notes for GenomeStudio Software 2.0, which includes the Genotyping v2.0 and Polyploid Genotyping v2.0 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.

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.

HumanOmniExpressExome-8 v1.0 Support Files

This download contains the gene annotation file (.zip) and minor allele frequencies file (.zip) for the HumanOmniExpressExome-8 v1.0 BeadChip.

HumanExome-12 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) files for the HumanExome-12 v1.0 BeadChip.

HumanKaryomap-12 v1.0 BeadChip Product Files for the NextSeq 550 System

Manifest file (*.bpm) and cluster file (*.egt) for the HumanKaryomap-12 v1.0 BeadChip compatible with the NextSeq 550 System.

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.

HumanOmniExpressExome-8 v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmniExpressExome-8 v1.1 BeadChip.

HumanOmni2.5Exome-8 v1.1 Support Files

Support files for the Infinium HumanOmni2.5Exome-8 v1.1 BeadChip.

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.

HumanCore-12 Support Files

This download contains the latest gene annotation file (.txt) for the HumanCore-12 v1.0 BeadChip.

BovineSNP50 v3.0 Product Files

This download contains the manifest file (.bpm and .csv) and cluster file (.egt) for the BovineSNP50 v3.0 BeadChip.

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.

HumanHT-12 v4.0 Gene Expression BeadChip Product Files

This download contains the manifest files (.bgx and .txt) and sample sheet (.csv) for the HumanHT-12 v4.0 Gene Expression BeadChip. These manifest files can be used with any version of BeadStudio.

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. 

Human610-Quad v1.0 Product Files

This download contains the Manifest (.bpm and .csv), cluster file (.egt) and product descriptor file (.xml) for the Human610-Quad v1.0 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

Make MUN ASE Batch Template (15004544 A)

This download contains a comma-separated values file as an example of the input to the Make MUN ASE Batch robot task when run in offline mode.

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.

BovineLD v2.0 Support Files

This download contains the annotation file (.csv)  BovineLD v2.0 BeadChip.

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.

Infinium HD Super Assay Sample Sheet Template (11310928 A)

This download contains the sample sheet template for the Infinium HD Super Assay.

KaryoStudio Software v1.4

Download includes the installers for updating KaryoStudio, the User Guide and the Release Notes for KaryoStudio v1.4

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.

Infinium Omni2.5-8 v1.3 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) files for the Infinium Omni2.5-8 v1.3 BeadChip. Use the manifest file appropriate for the reference genome you are using.

GeneSeek GGP Equine Product Files

This download contains the manifest files in BPM and CSV format and the cluster file for the GeneSeek GGP Equine array.

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.

HumanOmniZhongHua-8 v1.2 Product Files

This download contains the latest manifest files (.bpm and .csv), cluster file, and LIMS product descriptor file for the HumanOmniZhongHua-8 v1.2 BeadChip.

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."

WG DASL Assay Sample Sheet Template (330317 A)

This download contains a comma-separated values file you can use as a sample sheet template for the WG DASL Assay.

Infinium ImmunoArray-24 v2.0 Product Files

This download contains the latest manifest (.bpm and .csv), LIMS product descriptor file (.xml) and cluster file (.egt) for the Infinium ImmunoArray-24 v2.0 BeadChip. Use the manifest file appropriate for the reference genome you are using.

Infinium QC Array-24 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Infinium Exome-24 BeadChip Kit. Use the manifest file appropriate for the reference genome you are using.

HumanOmni1-Quad v1.0 Product Files

This download contains the Manifest File (.bpm and .csv), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanOmni1-Quad v1.0 DNA Analysis BeadChip.

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.

African American Admixture Panel Product Files

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation file for the GoldenGate African American Admixture Panel.

HumanOmniExpressExome-8 v1.2 Product Files

This download contains the manifest files in BPM and CSV format, the cluster file, and the LIMS product descriptor file for the HumanOmniExpressExome-8 v1.2 BeadChip.

Infinium OmniZhongHua-8 v1.3 Support Files

This download contains the latest product support files for the Infinium OmniZhongHua-8 v1.3 BeadChip.

EquineSNP50 v1.0 Product Files

This download contains the Manifest (.bpm), Cluster File (.egt), and SNP list (.xls) for the EquineSNP50 v1.0 DNA Analysis BeadChip.

Local Run Manager Software Release Notes

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

Infinium Omni2.5Exome-8 v1.3 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Infinium Omni2.5Exome-8 v1.3 BeadChip. Use the manifest file appropriate for the reference genome you are using.

HumanCytoSNP FFPE-12 v2.1 Product Support Files

This download contains the latest marker list (.txt) for the HumanCytoSNP FFPE-12 v2.1 BeadChip. This file is specific to the FFPE version of the CytoSNP-12 BeadChip and is used for processing restored FFPE samples. Do not use this file when processing non-FFPE samples.

GoldenGate ImportManualBatch DNA Template - noOPA (15004540 A)

This download contains a comma-separated values file to use as a template for the Illumina LIMS Import Manual Batch function to create a customized batch of DNA samples with no OPA from a single GoldenGate Assay project.

Sequencing Analysis Viewer v1.8.37 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from all HiSeq systems, HiSeq X, NextSeq, MiSeq, 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.

GeneSeek GGP GIGA-MUGA Product Files

This download contains the manifest files in BPM and CSV format and the cluster file for the GeneSeek GGP GIGA-MUGA array.

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.

DASL Cancer Panel Product Files

This download contains the manifest and content descriptor for the DASL Cancer Panel. (GS0006426)

Infinium Omni5Exome-4 v1.2 Support Files

This download contains product support files for the Infinium Omni5Exome-4 Kit.

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.

CytoSNP-850K v1.1 BeadChip Product Files for the NextSeq 550 System

Manifest files (.bpm and .csv), LIMS Product Descriptor File (.xml), and cluster file (.egt) for the CytoSNP-850K v1.1 BeadChip compatible with the NextSeq 550 System.

HumanHap300 Product File

This download is the the Manifest file (.bpm), Cluster File (.egt), and LIMS Product Descriptor (.xml) for the HumanHap300 BeadChip.

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”.

CytoSNP-850K v1.1 BeadChip Support Files for the iScan System

Product support files for the CytoSNP-850K v1.1 BeadChip compatible with the iScan System.

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.

CanineHD Product Files

This download contains the manifest (.bpm and .csv), cluster file (.egt), and product descriptor file (.xml) for the CanineHD BeadChip.

HumanCoreExome-12 v1.1 Support Files

This download contains the latest Demo Sample Sheet (.csv) and the Minor Allele Frequencies Summary (.zip) for the HumanCoreExome-12 v1.1 BeadChip.

Infinium OmniExpressExome-8 v1.4 Support Files

This download contains product support files for the Infinium OmniExpressExome-8 v1.4 BeadChip.

GoldenGate ImportManualBatch DNA Template (15004539 A)

This download contains a comma-separated values file to use as a template for the Illumina LIMS Import Manual Batch function to create a customized batch of DNA samples from a single GoldenGate Assay project.

Infinium Exome-24 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Infinium Exome-24 BeadChip Kit. Use the manifest file appropriate for the reference genome you are using.

HumanOmni2.5Exome-8 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxilliary files for the Infinium HumanOmni2.5Exome-8 v1.0 BeadChip.

HumanOmni2.5Exome-8 v1.0 Support Files

Support files for the Infinium HumanOmni2.5Exome-8 v1.0 BeadChip.

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.

VeraCode Sample Scan Setting Files

This zip file contains sample scan settings files for multiplex VeraCode GoldenGate Genotyping Assays: 48-plex, 96-plex, 144-plex, 192-plex, and 384-plex. In addition, instructions are provided for installing and using the scan setting files.

Infinium OmniZhongHua-8 v1.3 Product Files

This download contains the latest manifest files (.bpm and .csv), cluster file (.egt), and LIMS product descriptor file for the Infinium OmniZhongHua-8 v1.3 BeadChip. Use the manifest file appropriate for the reference genome you are using.

HumanOmni2.5S-8 v1.0 Multi-use Legacy Product Files

This download includes manifest (.bpm and .csv), cluster file (.egt) and LIMS product descriptor (.xml) for the HumanOmni2.5S-8 v1.0 Multi-Use Legacy BeadChip.

HumanOmni5Exome-4 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxilliary files for the Human Omni5Exome-4 v1.0 BeadChip.

HumanOmni2.5-Quad Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), and LIMS Product Descriptor (.xml) for the HumanOmni2.5-4 v1.0 DNA Analysis BeadChip. 

Infinium HumanMethylation450K v1.2 Product Files

Product files (bpm, csv, and header descriptor key files) for the HumanMethylation450 BeadChip.

GeneSeek GGP Bovine LD v4 Product Files

This download contains the manifest file (.bpm and .csv) and the strand report for the GeneSeek GGP Bovine LD v4 array.

CytoSNP-850K v1.1 FFPE Product Files

Manifest files (.bpm and .csv), and cluster files (.egt) for CytoSNP-850K v1.1 FFPE.

CytoSNP-850K BeadChip Product Files for the NextSeq 550 System

Manifest file (*.bpm) and cluster file (*.egt) for the CytoSNP-850K BeadChip compatible with the NextSeq 550 system.

Sequencing Analysis Viewer v1.8.46 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiSeq, NextSeq, HiScanSQ, HiSeq X, and all HiSeq systems. Download and unzip this file to install SAV for viewing sequencing runs on an offline computer. Changes associated with this version of the software are included in the software release notes. This SAV version requires Windows .NET Framework 4.5. If your system is using Windows .NET Framework 4, continue using SAV 1.8.37.

HumanOmni5-Quad v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmni5-Quad v1.0.

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.

Infinium MethylationEPIC Demo Data Set

An example data set of samples run with the Infinium MethylationEPIC array.

VeraCode ADME Core Panel SNP List

This download contains the SNP list for the VeraCode ADME Core Panel.

BovineHD Support Files

This download contains the mapping comment file (.txt) and annotation file (.csv) for the BovineHD BeadChip.

GC Content Polynomial Fit v1.4.6 C# Script for GenomeStudio

GC Content Polynomial Fit v1.4.6 C# Script for GenomeStudio

HumanOmni2.5S-8 v1.0 Product Files

This download includes the manifest (.bpm and .csv), cluster file (.egt) and product descriptor (.xml) for the HumanOmni2.5S-8 v1.0 Single-Use microarray.

Beeline Software v1.0

This download includes installers for the Beeline Software v1.0 and AutoConvert Software v1.6.

TruSeq Amplicon Support - Cancer Panel Manifest File Download

TruSeq Amplicon - Cancer Panel Manifest File (.txt)

OvineSNP50 v1.0 Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt) and Product Descriptor File(.xml) for the OvineSNP50 v1.0 DNA Analysis BeadChip.

HumanOmni2.5-8 v1.2 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) files for the HumanOmni2.5-8 v1.2 BeadChip.

bcl2fastq2 Conversion Software v2.17

This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2.17, 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 v2.17 can be used to convert BCL files from all Illumina sequencing systems running RTA version 1.18.54 and above. For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4.

Software installers are available in both *.rpm and *.tar.gz format. Installation instructions are provided in the Software Guide.

Bovine3K Product Files

This download contains the Manifest (.csv), Cluster File (.egt), and LIMS product descriptor for the Bovine3K Panel.

Human MicroRNA v2.0 Assay Pool Manifest

 

This download contains a binary manifest file for the Human MicroRNA v2.0 Assay Pool. Use this manifest file with BeadStudio 3. Annotation updated Oct 2008

 

HumanCoreExome-24 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanCoreExome-24 v1.0 BeadChip.

HumanCytoSNP-12 v2.0 Product Support Files

This set of files includes the product support files the CytoSNP-12 v2.0 including: .csv version of the manifest, GenomeStudio demo workspace, minor allele frequencies, physical and genetic coordinates, gene annotation files, simple marker list, build 36 to build 37 mapping information, demo sample sheet, gentrain sample sheet and markers-of-interest file. All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

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.

HumanHT-12 v4.0 Whole-Genome DASL HT Assay Product Files

This download contains a binary manifest files (.bgx and .txt) for the HumanHT-12 v4.0 Gene Expression BeadChip with the Whole-Genome DASL HT assay. This manifest file can be used with any version of GenomeStudio.

Infinium PsychArray v1.1 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Infinium PsychArray v1.1 BeadChip Kit. Use the manifest file appropriate for the reference genome you are using.

HumanCNV370-Duo v1.0 Product Files

This download contains the Manifest (.bpm) and Cluster File (.egt) for the HumanCNV370-Duo v1.0 DNA Analysis BeadChip. Infinium LIMS users, please note LIMS v1.2.0.18 is REQUIRED FOR PROCESSING this BeadChip.

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.

HumanImmuno BeadChip Product Support Files

This set of files includes the product support files for the HumanImmuno BeadChip including: GenomeStudio demo workspace, minor allele frequencies, gene annotation files, and simple marker list. Map positions are in build 36 coordinates.

Cardio-MetaboChip Product Support Files

This set of files includes the product support files for the Cardio-MetaboChip including: minor allele frequencies, gene annotation files, simple marker list. Map positions are in build 36 coordinates.

GeneSeek GGP Bos Indicus HD Product Files

This download contains the manifest files in BPM and CSV format, the cluster file, and the strand report for the GeneSeek GGP Box Indicus HD array.

BovineLD v1.1 Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), and LIMS product descriptor for the BovineLD v1.1.

GeneSeek GGP Bovine LD v3 Product Files

This download contains the manifest files in BPM and CSV format, cluster file, and strand report for the GeneSeek GGP Bovine LD v3 array.

Infinium PsychArray v1.1 Support Files

This download contains a file for UCSC browser (.bed), gene annotation file (.txt), demo data (.zip), sample sheet demo (.csv), reproducibility and heritability report (.csv), loci name to rsID conversion file (.txt), strand report (.txt), mapping comments file (.txt), physical and genetic coordinates file (.txt), population reports (.zip), legacy overlap file (.txt), missing legacy SNPs file (.txt), additional SNPs file (.txt), and prior product modification file (.txt) for the Infinium PsychArray v1.1 BeadChip Kit.

HumanExome-12 v1.2 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), and README file for the HumanExome-12 v1.2 BeadChip.

Make SUD Batch Template (15004546 A)

This download contains a comma-separated values file as an example of the input to the Make SUD Batch robot task when run in offline mode.

HumanOmniZhongHua-8 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the HumanOmniZhongHua-8 v1.0 BeadChip.

Human1M-Duo v3.0 Product Support Files

This set of files includes the product support files the 1M-Duo including: GenomeStudio demo workspace, minor allele frequencies, mapping information (build 36-->build 37), physical and genetic coordinates, gene annotation files, simple marker list, markers of interest file and sample sheets for the demo workspace and gentrain data (iControlDB). All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

iControlDB Download Package
This download contains the iControlDB client and user guide required for downloading genotyping data from the iControlDB.
Polyploid Genotyping Module Demo Dataset - Potato

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

HumanOmniZhongHua-8 v1.0 Support Files

This download includes demo data, .bed file, and minor allele frequencies.

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.

HumanOmni2.5-Quad Product Support Files

This set of files includes the product support files the Omni2.5-Quad including: GenomeStudio demo workspace, minor allele frequencies, mapping information (build 36-->build 37), physical and genetic coordinates, gene annotation files, simple marker list, markers-of-interest file, and sample sheets for the demo workspace and gentrain data (iControlDB). These support files are the same for the sinlge-use and multi-use versions of the Omni2.5-Quad. All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

Whole-Genome Gene Expression DASL HT Sample Sheet (15018363 A)

This download contains the sample sheet template for performing the Whole-Genome Gene Expression DASL HT Assay.

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.

HumanOmni5MExome-4 v1.1 Product Support Files

This download contains the latest gentrain and demo sample sheets (.csv) for the HumanOmni5MExome-4 v1.1 BeadChip.

BovineSNP50 v2.0 Product Files

This download contains the Manifest (.bpm and .xlsx) and Cluster File (.egt) for the BovineSNP50 v2.0 DNA Analysis BeadChip. Infinium LIMS users, please note the Product Descriptor file (.xml) is REQUIRED FOR PROCESSING this BeadChip.

Infinium BovineLD Product Descriptor File

Identifies the genotyping product for processing BeadChips in illumina LIMS

HumanCytoSNP FFPE-12 v2.1 Product Files

This download contains the latest manifest (.bpm and .csv) and cluster file (.egt) for the HumanCytoSNP FFPE-12 v2.1 BeadChip. These files are specific to the FFPE version of the CytoSNP-12 BeadChip and are used for processing restored FFPE samples. Do not use the files in this download when processing non-FFPE samples.

HumanOmni2.5-8 v1.2 Support Files

This download contains the latest sample sheet, demo sample sheet, strand report, reproducibility and heritability report, mapping comments, loci report, rsID, missing legacy SNPs, and additional SNPs, and gene annotation files for the HumanOmni2.5-8 v1.2 BeadChip.

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).

Infinium OmniExpressExome-8 v1.3 Product Files

This download contains the manifest files in BPM and CSV format, the cluster file, and the LIMS product descriptor file for the Infinium OmniExpressExome-8 v1.3 BeadChip.

CytoSNP-850K v1.1 BeadChip Support Files for the NextSeq 550 System

Product support files for the CytoSNP-850K v1.1 BeadChip compatible with the NextSeq 550 System.

Infinium Omni5-4 v1.1 Product Files

This downloads page contains the latest manifest files in BPM and CSV formats, the LIMS product descriptor file, and the cluster file for the Infinium Omni5-4 Kit.

Infinium PsychArray Product Files

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), mapping comments, prior product modifications, and auxiliary files for the Infinium PsychArray BeadChip Kit.

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.

DMAP Download Client Utility User Guide (15005597)

Instructions for installing and using the DMAP Download Client Utility to download DMAP files.

  • Decode File Client Setup 64 3.0.2 - Unzip and launch to install. Do not uninstall any previous versions of the client.
  • DMAP DLL Files - For the error "Error validating \xxx .dmap gz," refer to the installation instructions.
Infinium PsychArray Support Files

This download contains a sample sheet demo (.csv), reproducibility and heritability report, rsids (.txt), for the Infinium PsychArray BeadChip Kit.

Make SUD ASE Batch Template (15004545 A)

This download contains a comma-separated values file as an example of the input to the Make SUD ASE Batch robot task when run in offline mode.

GeneSeek GGP Potato Product Files

This download contains the manifest files in BPM and CSV format and the strand report for the GeneSeek GGP Potato array.

GenomeStudio Software 2009.2

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

HumanExome-12 v1.1 Support Files

This download contains support files for the HumanExome-12 v1.1 product.

Curator

This download contains the Curator install package and release notes. Curator is released as beta software. Please read the release notes for important installation details and our limited support policy for this beta pro.

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).

BovineLD v2.0 Product Files

This download contains the manifest files in BPM and CSV format, the cluster file, and the LIMS product descriptor file for the BovineLD v2.0 BeadChip.

HumanOmni2.5-8 v1.1 Support Files

This download contains the latest annotation file (.zip) for the HumanOmni2.5-8 v1.1 BeadChip.

BovineSNP50 v1.0 Product Files

This download contains the Manifest (.bpm), Cluster File (.egt), and markerlist (.txt) for the BovineSNP50 v1.0 DNA Analysis BeadChip.

MouseRef-8 v2.0 Product Files

This download contains the manifest files (.bgx and .txt) for the MouseRef-8 v2.0 Gene Expression BeadChip. This manifest files are to be used with BeadStudio 3.

bcl2fastq2 Conversion Software v2.18

This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2.18, 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 v2.18 can be used to convert BCL files from all Illumina sequencing systems running RTA version 1.18.54 and above, and replaces v2.17. For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4.

Software installers are available in both *.rpm and *.tarball format. Installation instructions are provided in the Software Guide.

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.

Infinium Omni5Exome-4 v1.3 Product Files

This download contains the manifest files (.bpm and .csv), cluster file, and LIMS product descriptor (.xml) file for the Infinium Omni5Exome-4 v1.3 Kit. Use the manifest file appropriate for the reference genome you are using.

Cancer SNP Panel Product Files

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Cancer SNP Panel.

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.

HumanCytoSNP-12 v2.1 Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanCytoSNP-12 v2.1 DNA Analysis BeadChip. 

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.

Human610-Quad v1.0 Product Support Files

This set of files includes the product support files the 610-Quad including: GenomeStudio demo workspace, minor allele frequencies, mapping information (build 36-->build 37), physical and genetic coordinates, gene annotation files, simple marker list, markers-of-interest file, and sample sheets for the demo workspace and gentrain data (iControlDB). All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.