Downloads

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

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

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).

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.

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

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

Example template the Sample Manifest file which is used to accession samples into LIMS for processing HumanMethylation 450 chips.

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.

Instructions for using the BeadScan Software.

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

This download contains the Manifest (.opa), BeadStudio Project (.bsc), and annotation files for the Bovine3K Panel.

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

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

This download contains the Manifest (.bpm and .xlsx) and Cluster File (.egt) for the BovineSNP50v2.0 DNA Analysis BeadChip. Infinium LIMS users, please note the Product Descriptor file (.xml) is REQUIRED FOR PROCESSING this BeadChip.

"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."

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

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

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

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

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

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

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.

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.

"This download contains an installer for cBot software version 1.4 (cBotSetupX86_1.4.36.0 file) providing new v8 recipes required for use with TruSeq Paired End Cluster Kit v3 and Flow Cell v3. To use TruSeq Single Read v3 kits, an update to the recipes is required. Please use the ""RecipeInstaller_1.0.13.0"" file to perform this update. This software should be installed solely on your cBot instrument and is user installable if upgrading from cBot software version 1.3. For additional details, please review the Release Notes and Install Notes for cBot 1.4 (available for individual download as .pdf files from this link) prior to installation."

This download contains the installer for cBot software version 1.5 (cBotSetupX86_1.5.12.0 file), providing new Rapid recipes required for use with Rapid Flow Cells. This software should be installed solely on your cBot instrument and is user installable if upgrading from cBot software version 1.4. For additional details, please review the Release Notes and Installation Notes (available as PDFs in the .zip file from this link) prior to installation.

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.

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.

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

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

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.

This download contains the latest manifest (.bpm and .csv), cluster file (.egt), and LIMS product descriptor (.xml) for the Cytogenetics Research Consortium (CRC) array.

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

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

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

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

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

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”.

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.

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.

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.

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

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

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.

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.

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

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

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.

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.

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.

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.

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.

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

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.

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

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

This download contains an update to the HiSeq Control Software (HCS), Real-Time Analysis (RTA) Software and Sequencing Analysis Viewing (SAV) Software. This release updates recipes and configurations required for use with TruSeq SBS v3 reagents and Flow Cell v3 and contains important bug fixes and stability enhancements for all users of HiSeq and HiScanSQ systems (running HCS1.4.5 and lower).

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).

<p><em>This download contains an update to the HiSeq Control Software (HCS), Real-Time Analysis (RTA) Software, Sequencing Analysis Viewing (SAV) and BaseSpace broker software.</em><span style="font-size: 9pt; line-height: 17pt;"></span></p> <p><strong>HCS 2.0.10 can be installed only on HiSeq systems currently running HCS 2.0.3 or HCS 2.0.5. HCS 2.0.10 is not yet available as an upgrade to HiSeq systems running HCS 1.5 or below. Installation of HCS 2.0.3 or HCS 2.0.5 by non-Illumina personnel onto HiSeq systems running HCS 1.5 or below will cause system failures and is not permitted.</strong></p>

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

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.

This download is the the BeadPool Manifest file (.bpm) for the HumanHap300 BeadChip.

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

This download contains the Manifest (.bpm), Cluster File (.egt), & CSV file (.csv), for the HumanOmniZhongHua-8 v1.0 DNA Analysis BeadChip.

This download contains a binary manifest file 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

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.

This download contains the Manifest (.bpm), 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.

This set of files includes the product support files the 1M-Duo including: .csv version of the manifest, 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.

This download contains the Manifest (.bpm), 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.

This set of files includes the product support files the 610-Quad including: .csv version of the manifest, 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.

This download contains the Manifest (.bpm), 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.

This set of files includes the product support files the 660W-Quad including: .csv version of the manifest, 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.

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.

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

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

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

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

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

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.

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.

This download contains the Manifest (.bpm), 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.

This download contains the Manifest (.bpm), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanCytoSNP-12 v2.1 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

This set of files includes the product support files the CytoSNP-12v2.1 including: .csv version of the manifest, 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.

This set of files includes the product support files the CytoSNP-12v2 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.

Product files for the Infinium HumanExome BeadChip. These files include the clusterfile (.egt), Manifest file (.bpm) and .xml file.

Product support files for the Infinium HumanExome BeadChip. These files include the .csv file which is a readable version of the manifest.

This download contains the product files for HumanExome BeadChip v1.1: Manifest (.bpm), cluster file (.egt) and product definition file (.xml).

This set of files contains support files for the HumanExome v1.1 product.

This download contains a binary manifest file for the HumanHT-12 v3 Gene Expression BeadChip. This manifest file can be used with any version of BeadStudio. Annotation updated March 2010

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

This download contains a binary manifest file for the HumanHT-12 v4 Gene Expression BeadChip. This manifest file can be used with any version of BeadStudio. Annotation updated April 2010

This download contains a binary manifest file in text format for the HumanHT-12 v4 Gene Expression BeadChip. Annotation updated April 2010.

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.

This download contains the manifest (.bpm) and CpG content list (.xls) for the HumanMethylation27 BeadChip.

Manifest v1.2 for Infinium HumanMethylation450 BeadChip

Content Descriptor file for the HumanMethylation 450K chip which is required to Accession Methylation beadchips into LIMS.

This set of files includes the product support files the Omni1-Quad including: .csv version of the manifest, GenomeStudio demo workspace, minor allele frequencies, physical and genetic coordinates, gene annotation files, simple marker list, build 36 -> build 37 mapping info, 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 Omni1-Quad. All files herein are in build 37 coordinates and correspond to the April 2011 manifest release.

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

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

This set of files includes the product support files the Omni1S-8 including: .csv version of the manifest, 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.

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

This download contains the Manifest (.bpm), 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.

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.

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

This set of files contains the manifest (.bpm), cluster file (.egt) and product definition file (.xml) for the HumanOmni2.5-8v1.0.

This set of files includes the product support files for the Omni2.5-8 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.

Product files for the Infinium HumanOmni2.5Exome BeadChip. These files include the clusterfile (.egt), Manifest file (.bpm) and .xml file.

Product support files for the Infinium HumanOmni2.5Exome BeadChip. These files include the .csv file which is a readable version of the manifest.

This download contains the Manifest (.bpm), Cluster File (.egt), and Product Descriptor File (.xml) for the HumanOmni2.5-4 v1.0 DNA Analysis BeadChip. For more information on the April 2011 Product Files release see FAQs.

This set of files includes the product support files the Omni2.5-Quad including: .csv version of the manifest, 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.

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

This download includes manifest (.bpm), cluster file (.egt) and product definition file (.xml) for the HumanOmni2.5S-8v1 Multi-use Legacy BeadChip.

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

This link includes product support files for the Omni2.5S-8 microarray including .csv manifest files, 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.

Product files for the Infinium Human Omni5Exome BeadChip.

Product Support files for the Infinium Human Omni5Exome BeadChip.

This download contains the latest manifest (.bpm and .csv) and LIMS product descriptor (.xml) for the HumanOmni5Exome-4 v1.1 BeadChip.

This download contains the latest cluster file (.egt) for the HumanOmni5MExome-4 v1.1 BeadChip.

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

This set of files contains the manifest (.bpm), cluster file (.egt) and product definition file (.xml) for the HumanOmni5-Quadv1.0.

This set of files includes the product support files for the Omni5-Quad 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.

This download contains the Manifest (.bpm), product descriptor file(.xml) and Cluster File (.egt) file for the HumanOmniExpress_FFPE v1.0 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.

This download contains the bed file and .csv version of the manifest.

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

This download contains the latest annotation file (.zip) for the HumanOmniExpress-12 v1.1 BeadChip.

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. For more information on the April 2011 Product Files release see FAQs.

Human OmniExpressExome Product Files Product files for the Infinium Human OmniExpressExome BeadChip.

Product Support files for the Infinium Human OmniExpressExome BeadChip.

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

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

This download contains the Manifest (.bpm), 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.

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.

This download contains a binary manifest file for the HumanRef-8 v3 Gene Expression BeadChip. This manifest file can be used with any version of BeadStudio. Annotation updated March 2010

This download contains a manifest file in text format for the HumanRef-8 v3 Gene Expression BeadChip. Annotation updated March 2010

This download contains a binary manifest file for the HumanWG-6 v3 Gene Expression BeadChip. This manifest file can be used with any version of BeadStudio. Annotation updated March 2010

This download contains a manifest file in text format for the HumanWG-6 v3 Gene Expression BeadChip. Annotation updated March 2010

This download contains the iControlDB client and user guide required for downloading genotyping data from the iControlDB.

Generic BeadChip-specific case reports which can be used if no case reports are available.

Instructions for uploading data to iControlDB using a phenotype information file.

<p>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.</p> <p>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).</p>

<p>The Illumina Experiment Manager v1.5.82 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).</p>

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

This download contains the Manifest (.bpm), cluster file (.egt) and product descriptor file (.xml) for the ImmunoChip.

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

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

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

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

Identifies the genotyping product for processing BeadChips in illumina LIMS

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

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

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

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

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

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

This download contains the Manifest (.bpm) 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.

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.

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.

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.

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

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

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

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 Software Updater v2.2.0.2 is Illumina&rsquo;s most recent release of MiSeq system software. The release includes the following updates: RTA v1.17.28, MCS v2.2, MiSeq Reporter v2.2, and MiSeq Recipes v2.2. For details on these updated packages, please see the Release Notes included in the MiSeq Updater v2.2.0.2 download. For full installation instructions, see the installation notes also included in the updater download. Please note that 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.

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

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

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.

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.

This download contains a binary manifest file in text format for the MouseRef-8 v2 Gene Expression BeadChip. Annotation updated March 2010

This download contains a binary manifest file for the MouseWG-6 v2 Gene Expression BeadChip. This manifest file can be used with any version of BeadStudio. Annotation updates March 2010.

This download contains a manifest file in text format for the MouseWG-6 v2 Gene Expression BeadChip. Annotation updated March 2010

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.

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.

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.

"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 &ndash; 500 with an Expanded Exome region at Chr 1 position 305 &ndash; 495 results in a 191 bp overlap and two 5 bp ""unique regions"" for the Exome product."

"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 &ndash; 500 with an Expanded Exome region at Chr 1 position 305 &ndash; 495 results in a 191 bp overlap and two 5 bp ""unique regions"" for the Exome product."

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.

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.

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.

"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 &ndash; 500 with an Expanded Exome region at Chr 1 position 305 &ndash; 495 results in a 191 bp overlap and two 5 bp ""unique regions"" for the Exome product."

Summary of the Nextera XT DNA sample preparation.

This download contains version 1.8 of the Off-Line Base Caller (OLB) software and documentation.

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.

These files contain the cluster files, beadpool manifest, gentrain reports, and sample sheet for the OmniExpress v1.1 product release

This download includes demo data, .bed file, .csv file, and MAF file.

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

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

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.

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.

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

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

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

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

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. Annotation updated March 2010.

This download contains a binary manifest file in text format for the RatRef-12 v1 Gene Expression BeadChip. Annotation updated March 2010

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.

Summary of changes introduced in SeqMonitor Service v1.0.80 and SeqMonitor App v1.0.

This spreadsheet helps with calculating the reagents and sequencing runs that are needed to arrive at the desired coverage for your experiment.

Shipping schedule change request form.

TruSeq Amplicon - Cancer Panel Manifest File (.txt)

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.

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

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

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.

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.

<p>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.</p> <p>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.</p> <p><strong>Note regarding biomarker patents and other patents unique to specific uses of products.</strong></p> <p>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&rsquo;s specific application.</p>

<p>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.</p> <p>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.</p> <p><strong>Note regarding biomarker patents and other patents unique to specific uses of products.</strong></p> <p>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&rsquo;s specific application.</p>

<p>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.</p> <p>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.</p> <p><strong>Note regarding biomarker patents and other patents unique to specific uses of products.</strong></p> <p>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&rsquo;s specific application.</p>

<p>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.</p> <p>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.</p> <p><strong>Note regarding biomarker patents and other patents unique to specific uses of products.</strong></p> <p>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&rsquo;s specific application.</p>

<p>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.</p> <p>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.</p> <p><strong>Note regarding biomarker patents and other patents unique to specific uses of products.</strong></p> <p>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&rsquo;s specific application.</p>

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

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.

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

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.

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

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

This download contains the Whole-Genome Gene Expression Direct Hybridization (DirHyb) Assay Sample Sheet Template

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.

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