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
HumanHap300 Product File

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

GoldenGate Linkage V Product Files

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

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.

HumanOmni5Exome-4 v1.0 Product Support Files

Product Support files for the Infinium Human Omni5Exome 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."

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.

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

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

Product File Download Client

This download contains a software application that enables you to download product manifest (bpm, opa, dap, oma) or product descriptor (.xml) files electronically.

PLINK Input Report Plug-in v2.1.3

This download contains a description of the PLINK Input Report Plug-in v2.1.3 for the GenomeStudio software.

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, Methylation v1.9, Protein Analysis v1.1, ChIP Sequencing v1.9, DNA Sequencing v1.9, and RNA Sequencing v1.9.

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.

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. 

 

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.

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.

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.

HumanWG-6 Product Files

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

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.

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.

 

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

 

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.

 

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.

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.

KaryoStudio Software v1.4

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

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.

MHC Panel Product Files

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

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.

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.

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.

HumanOmniZhongHua-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 HumanOmniZhongHua-8 v1.1.

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.

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.

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.

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”.

Infinium PsychArray Product Files

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

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

CanineHD Product Files

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

HumanImmuno BeadChip Kit Product Files

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

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.

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

Haploview Input Report Plug-in v2 for the GenomeStudio Genotyping Module (970-2009-015)

Haploview Input Report Plug-in v2 for the GenomeStudio Genotyping Module (970-2009-015)

Humancvd v1.0 Product Files

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

TruSeq Amplicon Support - Cancer Panel Manifest File Download

TruSeq Amplicon - Cancer Panel Manifest File (.txt)

HumanOmniExpressExome-8 v1.1 Support Files

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

ArrayExpress Data Submission Report Plug-in v2.0.0 for the GenomeStudio Gene Expression Module (970-2009-014)

Instructions for using the ArrayExpress Data Submission Report v2.0.0 plug-in with GenomeStudio.

Infinium HumanMethylation450K v1.2 Product Files

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

VeraCode ADME Core Panel SNP List

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

HumanOmni2.5-8 v1.1 Product Support Files

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

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.

Amplicon Viewer Installer

The Illumina Amplicon Viewer is a desktop tool to allow users to analyze their MiSeq Amplicon data. With the Illumina Amplicon Viewer, users can aggregate samples from multiple runs for data analysis and visualization. Minimum System Requirements: US–English Windows Vista or 7 Operating System; 32-bit system /4 GB AM or 64-bit system /8 GB RAM; Microsoft.Net Framework 4.0 or above; Microsoft Office Excel 2010 (recommended).

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.

cnvPartition Plug-in v3.2.0 for GenomeStudio

This download contains the installer and documentation for the cnvPartition CNV Analysis Plug-in v3.2.0 for GenomeStudio.

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.

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.

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.

HumanOmni5Exome-4 v1.0 Product Files
Product Files for the Infinium HumanOmni5Exome BeadChip.
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.

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.

Sample Stats Report Plug-in v2.3.5 for GenomeStudio

This download contains the installer and instructions for the Sample Stats Report Plug-in for GenomeStudio Software. This plug-in creates a report which computes the values of several useful metrics, such as Call Rate and Log R Ratio Standard Deviation, for all included probes for each sample selected for inclusion in the report.

PorcineSNP60 v2.0 Product Support Files

This download contains the Mapping Comment (.zip) for the PorcineSNP60 v2.0 BeadChip.

Genome Analyzer Support - Gencall Software Downloads

This download contains the source files, scripts, and documentation necessary for installing and running the Gencall software on a Windows or Linux operating system.

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.

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.

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.

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.

HumanOmniZhongHua-8 v1.0 Product Support Files

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

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.

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.

Cardio-MetaboChip Product Files

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

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 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.

TruSeq Exome Run Quality scripts

This package of scripts calculates various descriptive statistics to help you evaluate TruSeq Exome run quality. The package includes an installer script (install.sh). Documentation on how to install and run the scripts can be found in the TruSeq Exome Enrichment Kit guide and in the README file.

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.

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."

ADME Plug-in Setup v1.0.1.4

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

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.

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.

GX Custom Output Report GenomeStudio Plug-in v2.1 (970-2009-012)

This download contains documentation for the Gene Expression Custom Output Report v2.1.0 for the GenomeStudio GX Module.

Infinium HD Methylation SNP List

A list of SNPs that could potentially impact HM450 array results if present in the test population.

TruSight Tumor Product Files

These manifest files contain the list of targeted regions corresponding to the TruSight Tumor 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 set.

BCL2FASTQ Conversion Software 1.8.4
This download contains the software, release notes, and user guide for the 1.8.4. version of the Bcl2FastQ conversion software. The Bcl2FastQ conversion software is a tool to handle bcl conversion and demultiplexing. Version 1.8.4 has added ability to mask multiple adapter sequences per read, has standard Illumina adapter sequences included in the bcl2fastq installation, and the stringency of the adapter masking feature is now configurable.
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.

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.

GenomeStudio Software 2009.1

This download includes the installer, README, and Release Notes for the GenomeStudio 2009.1 Framework, and v1.1 of the following GenomeStudio Modules: Genotyping, Gene Expression, Methylation, Protein Analysis, ChIP Sequencing, DNA Sequencing, and RNA Sequencing.

BeadScan Software Addendum Version 3.0 (11206805)

Instructions for using the BeadScan Software.

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.

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.

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.

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.

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.

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.

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.

DASL Cancer Panel Product Files

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

MiSeq Software Updater

 

MiSeq Software Updater v2.5 is the most recent release of the MiSeq system software. This software release includes updates to MiSeq Control Software, MiSeq Reporter, and MiSeq Recipes. For details about these updated packages, see the MiSeq Updater v2.5 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: Do not use this software updater for the MiSeqDx.

 

Cancer SNP Panel Product Files

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

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.

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.

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.

BCD Manifest File

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

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.

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.

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.

Infinium HD Super Assay Sample Sheet Template (11310928 A)

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

Bovine3K Product Files

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

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.

NextSeq System Suite v1.2

 

The NextSeq System Suite 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 new folder structure for recipes and an updated RTA quality model (Q-table) for generating Q-scores. Version 1.2.2 improves run robustness, improves memory buffering, adds SAV to the System Suite, and improves the dual indexing recipe for high output reagent kits.

To install this update, download the software installer NextSeq System Suite v1.2, 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 hg19 Reference Genome

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

HumanExome-12 v1.0 Support Files

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

 

HumanExome-12 v1.2 Support Files

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

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.

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.

TruSeq Custom Enrichment Trial Kit Support - Regions BED file Downloads

This bed file and gene list contains information on the Targeted Exons in the TruSeq Custom Enrichment Trial Kit. The bed file can be loaded into UCSC Genome Browser to visualize specific target regions or to compare with other data of interest accessible via UCSC Browser's tables function. The gene list contains gene symbol and number of targeted exons per gene.

This BED file has 6 columns:
1 chromosome
2 chrStart (zero-based) first position of the feature
3 chrEnd (zero-based) last position of the feature
4 name (chromosome:chrStart-chrEnd:probecount)
5 length (chrEnd-chromStart)
6 strand (all targets mapped to the plus strand = +)

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.

HumanOmniExpressExome-8 v1.2 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 v1.2 BeadChip.

CytoSNP-850K BeadChip Product Files

Manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), and sample sheet (.xls) for the CytoSNP-850K BeadChip.

Infinium BovineLD BeadChip allele report

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

HumanMethylation27 Product Support Files

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

iControlDB Upload User Guide (11297381)
Instructions for uploading data to iControlDB using a phenotype information file.
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.

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. 

HumanMethylation27 Product Files

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

HumanCoreExome-12 v1.0 Support Files

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

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).

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.

GoldenGate Universal-12 Genotyping Assay Sample Sheet Template

This download contains a comma-separated values file to use as a sample sheet template for the GoldenGate Universal-12 Genotyping Assay.

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.

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

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

MCS v2.2.2 Optional Hotfix

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

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.

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.

iControlDB Download Package
This download contains the iControlDB client and user guide required for downloading genotyping data from the iControlDB.
Beeline Software v1.0

This download includes installers for the Beeline Software and AutoConvert Software.

HumanOmniExpressExome-8 v1.2 Support Files

This download contains the sample sheets (.csv), Reproducibility and Heritability Report, and minor allele frequencies for the HumanOmniExpressExome-8 v1.2 BeadChip.

GoldenGate Indexing ImportManualBatch Template (15012806 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 samples from a single GoldenGate Indexing Assay project.

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.

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.

HumanOmniExpress-12 v1.0 FFPE Product Support Files

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

Mouse LD Linkage Product Files

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

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.

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.

TruSeq Exome Enrichment Kit Support - Targeted Regions BED File Download

This gzipped file (TruSeq_exome_targeted_regions.hg19.chr.bed.gz) contains information on the Targeted Exons in the TruSeq Exome product (201,071 regions). It can be loaded into UCSC Genome Browser to visualize specific target regions or to compare with other data of interest accesible via UCSC Browser's tables function.

This BED file has 6 columns:
1 chromosome
2 chromStart (zero-based) first position of the feature
3 chromEnd (zero-based) first position after the feature
4 name (chromosome:chromStart-chromEnd:gene)
5 length (chromEnd-chromStart)
6 strand (all targets mapped to the plus strand = +)<

HumanOmniExpress-12 v1.0 Product Files

This download contains the Manifest (.bpm and .csv), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanOmniExpress-12 v1.0 DNA Analysis BeadChip. For more information on the Sept 2012 Product Files release see FAQs.

HumanMethylation450K v1.0 Content Descriptor File

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

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.

Infinium BovineLD BeadChip Workspace

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

GX Custom Output Report Plug-In v2.1.0 for the GenomeStudio Gene Expression Module

Instructions for installing the GX Custom Output Report v2.1.0 plug-in.

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.

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.

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.

CNV Region Report Plug-in v2.1.1 (970-2009-020)

This download contains the installer and documentation for the CNV Region Report Plug-in v2.1.1.

HumanCore-24 v1.0 Support Files

This download contains support files for the HumanCore-24 v1.0 BeadChip Kit.

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.

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 Form

Shipping schedule change request form.

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.

PorcineSNP60-v1.0

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

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.

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.

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
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.

Partek Plug-In for GenomeStudio

This is a GenomeStudio plug-in written my Partek for CNV analysis.

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.

Infinium BovineLD Product Descriptor File

Identifies the genotyping product for processing BeadChips in illumina LIMS

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.

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.

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.

iControlDB Product Template Files
Generic BeadChip-specific case reports which can be used if no case reports are available.
GenomeStudio Software 2009.2 Release Notes (11319658)

Summary of new features and known issues in the GenomeStudio Software 2009.2 release.

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.

TruSight DNA Amplicon Product Files

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

DMAP Download Client Utility User Guide (15005597)

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

HumanOmniZhongHua-8 v1.0 Product Files
This download contains the Manifest (.bpm and .csv), Cluster File (.egt), & LIMS Product Descriptor (.xml), for the HumanOmniZhongHua-8 v1.0 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.

Infinium HD Methylation Sample Sheet (15020628 A)

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

HumanKaryomap-12 v1.0 BeadChip Product Files

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

HumanCore-24 v1.0 Product Files

This download contains the latest manifest (.bpm and .csv), and cluster file (.egt) for the HumanCore-24 v1.0 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.

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

Methylation Custom Output Report Plug-In v2.0.0 for the GenomeStudio Methylation Module (970-2009-019)

Instructions for installing the Methylation Custom Output Report Plug-In v2.0.0 for the GenomeStudio Methylation Module.

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.

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. 

Merlin Input Report Plug-in v2.0.1 for GenomeStudio Software

Instructions for using the Merlin Input Report v2.0.1 plug-in for GenomeStudio software.

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.

Mouse MD Linkage Product Files

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

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.

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.

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.

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.

NextSeq System Suite v1.3

 

The NextSeq System Suite v1.3 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, 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 streamlines system shutdown and system restart procedures, and adds indications for software update and wash notifications.

To install this update, download the software installer NextSeq System Suite v1.3, 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.

 

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.

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.

ArrayExpress Data Submission Report Plug-in v1.0 (970-2008-002)

This download contains a description of the ArrayExpress Data Submission Report Plug-in v1.0 for the BeadStudio Gene Expression Module.

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.

BovineHD Product Support Files

This download contains the Mapping Comment (.zip) for the BovineHD.

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).

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.

HumanOmni2.5Exome-8 v1.1 Product Support Files
Product support files for the Infinium HumanOmni2.5Exome-8 v1.1 BeadChip.
HumanOmni2.5-8 v1.0 Product 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.

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.

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."

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.

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.

BCL2FASTQ Conversion Software

 

This download contains the software, release notes, and user guide for the bcl2fastq conversion software. The bcl2fastq conversion software is a tool to handle bcl conversion and demultiplexing.

Use the bcl2fastq 2.15.0 conversion software to convert NextSeq 500 or HiSeq X output. Version 2.15.0 is only for use with NextSeq and HiSeq X data. Use bcl2fastq 1.8.4 for MiSeq and HiSeq data conversion. The software is available for download in either an rpm or tarball (.tar.gz) format.

 

HumanCore-12 Support Files

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

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.

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.

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.

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.

HumanExome-12 v1.1 Support Files

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

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.

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.

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 v1.2 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.

 

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.

 

Illumina Experiment Manager v1.8

The Illumina Experiment Manager v1.8 is a desktop tool that guides you in building library plates and creating the sample sheet used for sequencing on the MiSeq, NextSeq, or HiSeq systems. Minimum System Requirements: Windows Vista or 7 Operating System; 32-bit system, 4 GB RAM or 64-bit system, 8 GB RAM; Microsoft.Net Framework 4.0 or above; Microsoft Office Excel (recommended).

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.

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.

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.

OncoArray-500K v1.0 Product Support Files

This download contains sample sheets (.csv) and a gene annotation file (*.txt) for the Infinium OncoArray-500K v1.0 BeadChip Kit.

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.

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.

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.

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.

Sequencing Analysis Viewer v1.8.37 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiSeq, HiSeq, HiSeq X, and NextSeq 500 Systems. 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.

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.

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.

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.

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.

bcl2fastq 2.15 Conversion Software

Use the bcl2fastq 2.15.0 conversion software to convert NextSeq 500 or HiSeq X output to standard FASTQ file formats for downstream analysis using third-party analysis solutions. Version 2.15.0 is only for use with NextSeq and HiSeq X data. Use bcl2fastq 1.8.4 for MiSeq and HiSeq data conversion. The software is available for download in either an rpm or tarball (.tar.gz) format. See the bcl2fastq 2.15 User Guide for complete instructions on installing from either of these packages.

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.

Sequencing Analysis Viewer v1.8.46 Software

This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiSeq, HiSeq, HiSeq X, and NextSeq 500 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.

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...".

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 product release.

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.

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.

 

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.

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.

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.

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.