Downloads

This is the Sequencing Downloads A-Z list. Use your browser's find function (CTRL-F on PCs, or Command-F on Macs) to search by keyword.

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

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

Description
 
File Info
Date
ADME Plug-in Setup v1.0.1.4
This download contains the ADME Plug-in Setup v1.0.1.4 installer.
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.
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: 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.
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.
ArrayExpress Data Submission Report Plug-in v2.0 (970-2009-014)
Instructions for using the ArrayExpress Data Submission Report v2.0.0 plug-in with GenomeStudio.
BCD Manifest File
Example template the Sample Manifest file which is used to accession samples into LIMS for processing HumanMethylation 450 chips.
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.
BeadScan Software
Instructions for using the BeadScan Software.
Beeline Software v1.0
This download includes installers for the Beeline Software and AutoConvert Software.
Bovine3K Product Files
This download contains the Manifest (.csv), Cluster File (.egt), and LIMS product descriptor for the Bovine3K Panel.
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.
BovineHD Product Support Files
This download contains the Mapping Comment (.zip) for the BovineHD.
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.
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.
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.
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."
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.
Cancer SNP Panel Product Files
This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Cancer SNP Panel.
CanineHD Product Files
This download contains the manifest (.bpm and .csv), cluster file (.egt), and product descriptor file (.xml) for the CanineHD BeadChip.
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.
Cardio-MetaboChip Product Files
This download contains the manifest file (.bpm), cluster file (.egt) and product descriptor file (.xml) for the Cardio-MetaboChip.
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.
CASAVA 1.8.1
This download contains the source files, scripts, and documentation necessary for installing and running the Consensus Assessment of Sequence and Variance (CASAVA) software, Version 1.8.1, on a Linux operating system. This version is an update on the CASAVA 1.8 release, and the changes are recorded in the Release Notes available in the documentation.
CASAVA 1.8.2
This download contains the source files, scripts, and documentation necessary for installing and running the Consensus Assessment of Sequence and Variance (CASAVA) software, Version 1.8.2, on a Linux operating system. This version is an update of the CASAVA 1.8.1 release to support Nextera dual-indexing, among others. The changes are recorded in the Release Notes available in the documentation.
cBot Software Installer, Installation Notes, and Release Notes

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.

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.
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.
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.
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.
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.
CytoSNP-850K Product Files
Manifest (.bpm and .csv), cluster file (.egt), LIMS product descriptor (.xml), and sample sheet (.xls) for the CytoSNP-850K BeadChip.
DASL Cancer Panel Product Files
This download contains the manifest and content descriptor for the DASL Cancer Panel. (GS0006426)
DMAP Decode File Download Utility v3.0.2
Instructions for installing and using the DMAP Download Client Utility to download DMAP files.
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
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.
GC Content Polynomial Fit v1.4.6 C# Script for GenomeStudio
GC Content Polynomial Fit v1.4.6 C# Script for GenomeStudio
Gencall Software
This download contains the source files, scripts, and documentation necessary for installing and running the Gencall software on a Windows or Linux operating system.
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”.
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.
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.
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.
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.
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.
GenomeStudio Software 2009.2
Summary of new features and known issues in the GenomeStudio Software 2009.2 release.
GenomeStudio Software 2009.2
Summary of new features and known issues in the GenomeStudio Software 2009.2 release.
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.
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.
GEO Data Subm. Rpt. GenomeStudio Plug-in v2.0 (970-2009-013)
Instructions for installing the GX Custom Output Report v2.1.0 plug-in.
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.
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.
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.
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.
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.
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.
GoldenGate Linkage V Product Files
This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the GoldenGate Linkage V Panel Set.
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.
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.
Haploview Input Report GenomeStudio Plug-in v2.0 (970-2009-015)
Haploview Input Report Plug-in v2 for the GenomeStudio Genotyping Module (970-2009-015)
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).
HCS 2.0.12/RTA 1.17.21.3/SAV 1.8.20 Software
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 1000/2000 systems for customers who are 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 upgrading these HiSeq 1000/2000 systems. The software can be installed directly by customers on HiSeq 1500/2500 systems.

  • High level summary:
    • All HiSeq systems
      • Option to send sequencing, health and run monitoring data to BaseSpace
      • Option to reduce the data footprint >2x
      • Stability and reliability improvements
    • HiSeq 1500/2500 systems only
      • Rapid Run support
HiSeq Analysis Software hg19 Reference Genome
This download contains the human reference genome hg19 from UCSC for the HiSeq Analysis Software (tar).
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.
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.
Human Whole-Genome DASL HT binary manifest file (.txt)
This download contains a binary manifest file in text format for the HumanHT-12 v4 Gene Expression BeadChip with the Whole-Genome DASL HT assay. This manifest file can be used with any version of GenomeStudio. Annotation updated April 2010.
Human Whole-Genome DASL HT Product Files
This download contains a binary manifest files (.bgx and .txt) for the HumanHT-12 v4 Gene Expression BeadChip with the Whole-Genome DASL HT assay. This manifest file can be used with any version of GenomeStudio.
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.
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.
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.
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.
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.
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.
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.
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.
HumanCore-12 v1.0 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanCore-12 v1.0 BeadChip.
HumanCoreExome-12 v1.0 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanCoreExome-12 v1.0 BeadChip.
HumanCoreExome-12 v1.0 Product Support Files
This download contains the latest annotation file (.zip) for the HumanCoreExome-12 v1.0 BeadChip.
HumanCoreExome-12 v1.1 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanCoreExome-12 v1.1 BeadChip.
HumanCoreExome-12 v1.1 Product 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.
Humancvd v1.0 Product Files
This download contains the Manifest (.bpm) and Cluster File (.egt) for the HumanCVD v1.0 DNA Analysis BeadChip.
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.
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.
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.
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.
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. 
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. 
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.
HumanExome BeadChip Product Support Files
Product support files for the Infinium HumanExome BeadChip. These files include the .csv file which is a readable version of the manifest.
HumanExome BeadChip v1.1 Product Files
This download contains the product files for HumanExome BeadChip v1.1: Manifest (.bpm and .csv), cluster file (.egt) and product definition file (.xml).
HumanExome-12 v1.0 BeadChip Product Files
Product files for the Infinium HumanExome-12 v1.0 BeadChip. These files include the clusterfile (.egt), Manifest file (.bpm) and .xml file.
HumanExome-12 v1.1 Product Support Files
This set of files contains support files for the HumanExome-12 v1.1 product.
HumanExome-12 v1.2 Product Files
This download contains the latest cluster file (.egt), manifest file (.bpm and .csv), and LIMS product descriptor (.xml) for the HumanExome-12 v1.2 BeadChip.
HumanExome-12 v1.2 Product Support Files
This download contains the sample sheets (.csv), the gene annotation file (.txt) Reproducibility and Heritability Report, and minor allele frequencies for the HumanExome-12 v1.2 BeadChip.
HumanHap300 Product File
This download is the the Manifest file (.bpm), Cluster File (.egt), and LIMS Product Descriptor (.xml) for the HumanHap300 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
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.
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.
HumanImmuno BeadChip Product Files
This download contains the manifest (.bpm), cluster file (.egt) and product descriptor file (.xml) for the HumanImmuno BeadChip.
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.
HumanKaryomap-12 v1.0 Product Files
Manifest (.bpm) and cluster file (.egt) for the HumanKaryomap-12 v1.0 BeadChip.
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.
HumanMethylation27 Product Files
This download contains the manifest (.bpm) for the HumanMethylation27 BeadChip.
HumanMethylation27 Product Support Files
This download contains the content list (.xlsx) for the HumanMethylation27 BeadChip.
HumanMethylation450v1 15017482 C
Content Descriptor file for the HumanMethylation 450K chip which is required to Accession Methylation beadchips into LIMS.
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.
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.
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.
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.
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.
HumanOmni2.5-8 v1.0 Product Files
This set of files contains the manifest (.bpm and .csv), cluster file (.egt) and product descriptor file (.xml) for the HumanOmni2.5-8 v1.0.
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.
HumanOmni2.5-8 v1.1 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanOmni2.5-8 v1.1 BeadChip.
HumanOmni2.5-8 v1.1 Product Support Files
This download contains the latest annotation file (.zip) for the HumanOmni2.5-8 v1.1 BeadChip.
HumanOmni2.5Exome-8 v1.0 Product Files
Product files for the Infinium HumanOmni2.5Exome-8 v1.0 BeadChip. These files include the Cluster File (.egt), Manifest File (.bpm and .csv) and LIMS Product Descriptor (.xml).
HumanOmni2.5Exome-8 v1.0 Product Support Files
Product support files for the Infinium HumanOmni2.5Exome-8 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. 
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.
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.
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.
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.
HumanOmni2.5S-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
HumanOmni5Exome-4 v1.0 Product Files
Product Files for the Infinium Human Omni5Exome BeadChip.
HumanOmni5Exome-4 v1.0 Product Support Files
Product Support files for the Infinium Human Omni5Exome BeadChip.
HumanOmni5Exome-4 v1.1 Product Files
This download contains the latest Manifest (.bpm and .csv), LIMS product descriptor (.xml), and Cluster File for the HumanOmni5Exome-4 v1.1 BeadChip.
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.
HumanOmni5-Quad v1.0 Product Files
This set of files contains the manifest (.bpm and .csv), cluster file (.egt) and LIMS product descriptor (.xml) for the HumanOmni5-Quad v1.0.
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.
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 FFPE Product Support Files
This download contains the HumanOmniExpress-12 v1.0 FFPE .bed file.
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. 
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.
HumanOmniExpress-12 v1.1 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanOmniExpress-12 v1.1 BeadChip.
HumanOmniExpress-12 v1.1 Product Support Files
This download contains the latest annotation file (.zip) for the HumanOmniExpress-12 v1.1 BeadChip.
HumanOmniExpress-24 v1.0 Product Files
This download contains the latest manifest (.bpm and .csv ) and cluster files(.egt) and sample sheets (.csv) for the HumanOmniExpress-24 v1.0 BeadChip.
HumanOmniExpressExome Product Files
HumanOmniExpressExome Product Files Product files for the Infinium Human OmniExpressExome BeadChip.
HumanOmniExpressExome Product Support Files
Product Support files for the Infinium Human OmniExpressExome BeadChip.
HumanOmniExpressExome-8 v1.1 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanOmniExpressExome-8 v1.1 BeadChip.
HumanOmniExpressExome-8 v1.1 Product Support Files
This download contains the latest annotation file (.zip) for the HumanOmniExpressExome-8 v1.1 BeadChip.
HumanOmniExpressExome-8 v1.2 Product Files
This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the HumanOmniExpressExome-8 v1.2 BeadChip.
HumanOmniExpressExome-8 v1.2 Product Support Files
This download contains the sample sheets (.csv), Reproducibility and Heritability Report, and minor allele frequencies for the HumanOmniExpressExome-8 v1.2 BeadChip.
HumanOmniExpressv1.0 Product Support Files: Sept 2012 Release
This set of files includes the product support files for the OmniExpress including: .csv version of the manifest, 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.
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.
HumanOmniZhongHua-8 v1.0 Product Support Files
This download includes demo data, .bed file, and minor allele frequencies.
HumanOmniZhongHua-8 v1.1 Product Files
This download contains HumanOmniZhongHua-8 v1.1 manifest files (.bpm and .csv) and a cluster file (.egt) used for analysis.
HumanWG-6 Product Files
This download contains the HumanWG-6 manifest (BGX and TXT).
iControlDB Download Package
This download contains the iControlDB client and user guide required for downloading genotyping data from the iControlDB.
iControlDB Product Template Files
Generic BeadChip-specific case reports which can be used if no case reports are available.
iControlDB Upload Package
Instructions for uploading data to iControlDB using a phenotype information file.
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.
Illumina Experiment Manager v1.4.75

Note: Use this IEM v1.4.75 to generate sample sheets for use with CASAVA or AVC, otherwise use IEM 1.5.82 or later to generate your sample sheets.

The Illumina Experiment Manager is a desktop tool that guides you in building library plates and creating the sample sheet used for sequencing on the MiSeq 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).

Illumina Experiment Manager v1.6.0

The Illumina Experiment Manager v1.6.0 is a desktop tool that guides you in building library plates and creating the sample sheet used for sequencing on the MiSeq 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).

Illumina Sequencers Support - Configuring Virus Scanner Software Download
Explains how to set up virus scanners on instrument control computers for HiSeq, HiScanSQ, MiSeq and Genome Analyzer, such that they do not degrade or harm system performance
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.

Illumina Worklist Manager v1.0.15 Software Installer

This installer can be used to install Illumina Worklist Manager v1.0.15 to create a sample sheet to use with all the MiSeqDx IVD assays.

Infinium BovineLD BeadChip allele report
This download contains the allele report for the BovineLD DNA Analysis BeadChip.
Infinium BovineLD BeadChip Workspace
This download contains the complete workspace for the BovineLD DNA Analysis BeadChip
Infinium BovineLD Product Descriptor File
Identifies the genotyping product for processing BeadChips in illumina LIMS
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.
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.
Infinium HD Methylation SNP List
A list of SNPs that could potentially impact HM450 array results if present in the test population.
Infinium HD Super Assay Sample Sheet Template (11310928 A)
This download contains the sample sheet template for the Infinium HD Super Assay.
Infinium HumanMethylation450 v1.2 Product Files
Product files (bpm, csv, and header descriptor key files) for the HumanMethylation450 BeadChip.
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.
Infinium PsychArray Product Files
This download contains the latest manifest (*.bpm and *.csv) and cluster file (*.egt) for the Infinium PsychArray BeadChip Kit.
Infinium PsychArray Product Support Files
This download contains a sample sheet demo (.csv), reproducibility and heritability report, rsids (.txt), for the Infinium PsychArray BeadChip Kit.
KaryoStudio Software v1.4
Download includes the installers for updating KaryoStudio, the User Guide and the Release Notes for KaryoStudio v1.4
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.
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.
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.
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.
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.
Merlin Input Report Plug-in v2.0.1 (970-2008-005)
Instructions for using the Merlin Input Report v2.0.1 plug-in for GenomeStudio software.
Methylation Custom Output Report Plug-in v2.0.0 (970-2009-019)
Instructions for installing the Methylation Custom Output Report Plug-In v2.0.0 for the GenomeStudio Methylation Module.
MHC Panel Product Files
This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the MHC Panel.
MiSeq Reporter Installer
MiSeq Reporter is the bioinformatics data analysis software built into the MiSeq. This software is available as a standalone software for installation on a Windows workstation.
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.

MiSeq Software Updater

MiSeq Software Updater 2.4.1 is the most recent release of the MiSeq system software. This software, when used with MiSeq v3 reagents, offers a significant reduction in run time, with no change in the operation of the MiSeq instrument. This release includes updates to MiSeq Control Software, MiSeq Reporter, and RTA. For details about these updated packages, see the MiSeq Updater v2.4.1 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.

Mouse LD Linkage Product Files
This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Mouse LD Linkage Panel.
Mouse MD Linkage Product Files
This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Mouse MD Linkage Panel.
MouseRef-8 v2 binary manifest file (.bgx)
This download contains a binary manifest file for the MouseRef-8 v2 Gene Expression BeadChip. This manifest file is to be used with BeadStudio 3. Annotation updated April 2008.
MouseRef-8 v2 binary manifest file (.txt)
This download contains a binary manifest file in text format for the MouseRef-8 v2 Gene Expression BeadChip. Annotation updated March 2010
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.
MouseWG-6 v2.0 Gene Expression BeadChip Product Files
This download contains the manifest files (.bgx and .txt) for the MouseWG-6 v2 Gene Expression BeadChip. These manifest file can be used with any version of BeadStudio.
Nextera Rapid Capture Exome Probe Manifest
This download contains the Nextera Rapid Capture Exome probe manifest in the format required by the HiSeq Analysis Software. It lists the 412,006 enrichment probes with chromosome location in GRCh37/hg19.
Nextera Rapid Capture Exome Probe Manifest v1.2
This download contains the Nextera Rapid Capture Exome probes manifest v1.2 in the format required by the HiSeq Analysis Software. It lists the 425,437 enrichment probes with start and stop chromosome locations in GRCh37/hg19.
Nextera Rapid Capture Exome Targeted Regions Manifest (.bed)
This download contains the Nextera Rapid Capture Exome regions manifest in the standard BED format. It lists the 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.
Nextera Rapid Capture Exome Targeted Regions Manifest (.txt)
This download contains the Nextera Rapid Capture Exome regions manifest in the format required by the HiSeq Analysis Software. It lists the 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.
Nextera Rapid Capture Exome Targeted Regions Manifest v1.2 (.bed)
This download contains the Nextera Rapid Capture Exome regions manifest v1.2 in the standard BED format. It lists the 214,126 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.
Nextera Rapid Capture Exome Targeted Regions Manifest v1.2 (.txt)
This download contains the Nextera Rapid Capture Exome regions manifest v1.2 in the format required by the HiSeq Analysis Software. It lists the 214,126 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.
Nextera Rapid Capture Exome Targeted Regions Manifest v1.2 ReadMe
This download contains is a ReadMe document describing the new Nextera Rapid Capture Exome manifest v1.2 files
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."
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."
Nextera Rapid Capture Expanded Exome Probe Manifest
This download contains the Nextera Rapid Capture Expanded Exome probe manifest in the format required by the HiSeq Analysis Software. It lists the 347,517 enrichment probes with chromosome location in GRCh37/hg19.
Nextera Rapid Capture Expanded Exome Targeted Regions Manifest (.bed)
This download contains the Nextera Rapid Capture Expanded Exome regions manifest in the standard BED format. It lists the 201,071 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.
Nextera Rapid Capture Expanded Exome Targeted Regions Manifest (.txt)
This download contains the Nextera Rapid Capture Expanded Exome regions manifest in the format required by the HiSeq Analysis Software. It lists the 201,071 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19.
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."
OFF-LINE BASE CALLER 1.8 SOFTWARE
This download contains version 1.8 of the Off-Line Base Caller (OLB) software and documentation.
OFF-LINE BASE CALLER 1.9.4 SOFTWARE
This download contains the latest version of the Off-Line Base Caller (OLB) software (version 1.9.4) and related documentation to use with the Genome Analyzer SCS2.10 and RTA1.13 software. Important: use OLB1.9.4 with SCS2.9/RTA1.9 software and HCS1.5/RTA1.13 software.
OmniExpress Product Support Files
These files contain the cluster files, beadpool manifest, gentrain reports, and sample sheet for the OmniExpress v1.1 product release
OncoArray-500K v1.0 Product Files
This download contains the latest manifest (*.bpm and *.csv) and cluster file (*.egt) for the Infinium OncoArray-500K BeadChip.
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.
Partek Plug-In for GenomeStudio
This is a GenomeStudio plug-in written my Partek for CNV analysis.
Pipeline 1.3.2
This download contains the source files necessary for installing and running the Genome Analyzer Pipeline Analysis software on a Linux operating system. This release is compatible and intended for use with IPAR 1.3 and SCS 2.3.
Pipeline 1.5.1
This download contains the source files necessary for installing and running the Genome Analyzer Pipeline Analysis software on a Linux operating system. This release is compatible and intended for use with SCS 2.5. The fft_lib.zip package is only required if the FFT library has not been installed previously.
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.
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.
PorcineSNP60 v2.0 Product Support Files
This download contains the Mapping Comment (.zip) for the PorcineSNP60 v2.0 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.
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.
RatRef-12 v1.0 binary manifest file (.txt and .bgx)
This download contains a binary manifest file in text format for the RatRef-12 v1.0 Gene Expression 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.
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.
Sequencing Analysis Viewer v1.8.36 Software
This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiSeq, HiSeq, 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.
Sequencing Coverage Calculator
This spreadsheet helps with calculating the reagents and sequencing runs that are needed to arrive at the desired coverage for your experiment.
Ship Schedule Form
Shipping schedule change request form.
TruSeq Amplicon - Cancer Panel Manifest File
TruSeq Amplicon - Cancer Panel Manifest File (.txt)
TruSeq Custom Amplicon Control Manifest ACP1
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.
TruSeq Custom Enrichment Trial Kit Regions BED File

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 = +)

TruSeq Exome Enrichment Kit Targeted Regions BED File

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 = +)<

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

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.

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.

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.

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.

TruSight One Sequencing Panel Product Files

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.

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.

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.

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.

V2 Human MicroRNA Assay Pool Manifest (.bgx)
This download contains a binary manifest file for the v2 Human MicroRNA Assay Pool. This manifest file is to be used with BeadStudio 3. Annotation updated Oct 2008
V2 Mouse MicroRNA Assay Pool Manifest (.bgx)
This download contains a binary manifest file for the v2 Mouse MicroRNA Assay Pool. This manifest file is to be used with BeadStudio 3. Annotation updated Oct 2008.
VeraCode ADME Core Panel SNP List
This download contains the SNP list for the VeraCode ADME Core Panel.
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.
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.
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.
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.
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.