1. Genome Sequencer FLX System Software Manual, version 2.3 Part A: GS Sequencer and Other On-Instrument Software October 2009.
2. Software downloads for NextSeq 500 instrument software. Use the Manual Update. For conversion of data generated on Illumina sequencing systems using.

1. Sony Psp 3001 System Software Manual
2. System Software Meaning
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Roche/454 Genome Sequencer FLX Assembler, Mapper. The 454/Roche Genome Sequencer FLX System software contains tools for data. 454 Homepage; Software Manual.

. Part of the book series (MIMB, volume 1034) Abstract Next-generation sequencing (NGS) of HLA class I and II loci (HLA-A, HLA-B, HLA-C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPB1) is described here in detail using the 454 Life Sciences GS FLX System and Titanium chemistry.

An overview of the protocol with our experience on sequence performance efficiencies, read depth and ambiguity analyses using the GS FLX System are also presented. A total of 14 HLA primer pairs with multiplex identifiers (MIDs) are used in clonal, amplicon-based pyrosequencing of up to 44 samples per plate using the GS FLX. Genotype assignment and ambiguity reduction ­analysis is performed using Conexio Assign ATF 454 software.

Clonal NGS gives a significant reduction in genotyping ambiguity during analysis of the highly complex HLA system. Acknowledgments The authors would like to thank Henry Erlich, Martha Ladner, David Noonan, and Melinda Rastrou for their thoughtful reading of the manuscript. We would also like to acknowledge Damian Goodridge for the development of the genotyping software, and Kazu Osoegawa, Martha Ladner, Franziska Cohen, Sherry Hawbecker, David Noonan for setting this system up and sequencing all the samples in the CHORI lab. We would also like to acknowledge Priscilla Moonsamy and Bryan Hoglund for their contributions to initial development of primers and protocols. Trachtenberg is supported in part by NIH grants 2UO1AI067068 and 2P01CA111412.

.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 page. '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.' This download contains the Nextera Rapid Capture Exome targeted regions manifest files (.txt and.bed), and the exome probe manifest.

The targeted regions manifest files list the 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19. The exome probe manifest file lists the 412,006 enrichment probes with chromosome location in GRCh37/hg19. The Nextera Rapid Capture Exome Targeted Regions Manifest and the Nextera Rapid Capture Exome Probe Manifest files are in.txt format. This format is required by the HiSeq Analysis Software. This manifest file contains the list of targeted regions corresponding to the TruSight Autism Content Set. This file is used by Illumina Experiment Manager (v1.4 or greater) and MiSeq Reporter Software (v2.1 or greater) for the analysis of TruSight Autism set.

This bed file contains information on the TruSight Autism Content Set. The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information. Note regarding biomarker patents and other patents unique to specific uses of products. Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents.

Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application. Illumina no longer accepts orders for TruSight Autism. The recommended replacement product is the TruSight One Sequencing Kit. Content from the TruSight Autism panel is avaialble in the comprehensive. Illumina remains committed to providing you with high-quality support and service. This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2.19.1, which can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. This software requires a Linux operating system.

The bcl2fastq2 Conversion Software v2.19.1 can be used to convert BCL files from MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq sequening systems. For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4. The software is available as an RPM (.rpm) for installation on CentOS/RedHat Linux distributions. A tarball (.tar.gz) of the source code is also available for compilation on other Linux distributions. Installation instructions are provided in the Software Guide. This download contains the software, release notes, and user guide for bcl2fastq Conversion Software v1.8.4, which can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. This software requires a Linux operating system.

The bcl2fastq Conversion Software v1.8.4 software can be used to convert BCL files from MiSeq and HiSeq sequencing systems running RTA versions earlier than 1.8. The bcl2fastq Conversion Software v1.8.4 added the ability to mask multiple adapter sequences per read and configure stringency for the adapter masking feature. The software includes standard Illumina adapter sequences. 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. The NextSeq System Suite v2.0 is the most recent release of the NextSeq system software. The NextSeq System Suite is user-installable. This release includes updates to the NextSeq Control Software and NextSeq Service Software. Changes include support for BeadChip scanning functionality on NextSeq 550 systems only.

NCS v2.0 is compatible with NextSeq 500 systems. NextSeq 500 system users will not observe any functional differences between NCS v2.0 and NCS v1.4. NCS 2.0 is not compatible with v1 reagents. Continue using NCS v1.3.2 with v1 reagents. To install this update, download the software installed NextSeq System Suite v2.0, and copy it to the NextSeq desktop or an accessible network location. From NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. Before installing the update, first read Important Information About Updating NCS v2.0.

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. 1988 Apr;2(3):231-9. 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 (NexteraRapidCaptureDemoData) 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 (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 NexteraRapidCaptureDemoData. This download contains an update to the HiSeq Control Software (HCS), Real-Time Analysis (RTA) software, Sequencing Analysis Viewing (SAV), and BaseSpace broker software.

Recommended for all HiSeq systems (not compatible with HiScan SQ systems at this time). ATTENTION: Software installation on HiSeq 1000 and HiSeq 2000 systems when upgrading from HCS 1.5.15.1 or earlier versions must be completed by an Illumina Support representative.

Please contact Illumina Technical Support or your Illumina FAS for assistance with the software upgrade. You can install the software without assistance on HiSeq 1500 and HiSeq 2500 systems. This download contains the Nextera Rapid Capture Expanded Exome targeted regions manifest files (.txt and.bed), and the exome probe manifest. The targeted regions manifest files list the 201,071 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19. The expanded exome probe manifest file lists the 347,517 enrichment probes with chromosome location in GRCh37/hg19.

The Nextera Rapid Capture Expanded Exome Targeted Regions Manifest and the Nextera Rapid Capture Expanded Exome Probe Manifest files are in.txt format. This format is required by the HiSeq Analysis Software. The NextSeq System Suite v2.0.2 is the most recent release of the NextSeq system software. The NextSeq System Suite is user-installable.

This release includes updates to the NextSeq Control Software and Real-Time Analysis (RTA2) software. Changes include an update for BeadChip part numbers on NextSeq 550 systems only.

RTA2 has been updated to improve demultiplexing performance for low-plexity samples. NCS 2.0.2 is not compatible with v1 reagents. Continue using NCS v1.3.2 with v1 reagents.

To install this update, download the software installed NextSeq System Suite v2.0.2, and copy it to the NextSeq desktop or an accessible network location. From NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. 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. The NextSeq System Suite v1.3.2 is user-installable. This release includes updates to the NextSeq Control Software, RTA2, NextSeq Service Software, NextSeq recipes, and the BaseSpace Broker.

Changes include a reduction in template loading volume and a flow cell recovery workflow. Version 1.3.2 is compatible with v1 reagents, streamlines system shutdown and restart procedures, and adds indications for software update and wash notifications. To install this update, download the software installer NextSeq System Suite v1.3.2, and copy it to the NextSeq desktop or an accessible network location.

From the NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. Before installing the update, first read Important Information About Updating Your Software. This download contains the software, release notes, and software guide for the bcl2fastq2 Conversion Software v2.20.0, which can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis. This software requires a Linux operating system. The bcl2fastq2 Conversion Software v2.20.0 can be used to convert BCL files from MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq sequening systems.

For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4. The software is available as an RPM (.rpm) for installation on CentOS/RedHat Linux distributions. A tarball (.tar.gz) of the source code is also available for compilation on other Linux distributions. Installation instructions are provided in the Software Guide. The NextSeq System Suite v1.4 is user-installable. This release includes updates to the NextSeq Control Software, RTA2, NextSeq Service Software, NextSeq recipes, and the BaseSpace Broker. Changes include support for v2 reagent kits.

Version 1.4 enables BaseSpace run monitoring, reagent purging, and an updated RTA quality model (Q-table) for generating Q-scores for v2 reagents. NCS v1.4 is not compatible with v1 reagents. Continue using NCS v1.3.2 with v1 reagents.

To install this update, download the software installer NextSeq System Suite v1.4, and copy it to the NextSeq desktop or an accessible network location. From the NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update. Before installing the update, first read Important Information About Updating Your Software. For details about MiSeq Software Updater v2.6, see the. For full installation instruction, see the Installation Notes included in the Updater download package. This software release continues to use the Reference Genomes v1.1.0.0 for MiSeq.

If you have previously installed this version of the Reference Genomes, there is no need to update the genomes again. Note: The software updater can also be installed in the RUO drive of MiSeqDx instruments with dual boot configuration. If you are not sure if your instrument has the dual boot upgrade, contact Illumina Technical Support. The download contains an update to the HiSeq Software Suite and includes new versions of HiSeq Control Software (HCS), Real-Time Analysis (RTA), Recipe Fragments, Sequencing Analysis Viewer (SAV), and the BaseSpace Broker.

This software includes support for Rapid Run mode using HiSeq Rapid v2 chemistry and an update to the maintenance wash to support only maintenance wash solution (Tween 20 and ProClin 300) protocol. This software is for all HiSeq systems except HiSeq X and HiScanSQ. Download and review the customer release notes for details about this release.

This manifest file contains the list of targeted regions corresponding to the TruSight One Sequencing Panels. 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 Panels. This bed file contains information on the TruSight One Sequencing Panels. 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. '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.' The NextSeq System Suite v2.1.2 is the most recent release of the NextSeq system software. The NextSeq System Suite is user-installable. This release includes updates to the NextSeq Control Software and Real-Time Analysis (RTA) software. To install this update, download the software installed NextSeq System Suite v2.1.2, and copy it to the NextSeq desktop or an accessible network location. From NextSeq Control Software Manage Instrument screen, use the Manual Update command to install the update.

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 9IconInstructions”. 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. Access to software that runs separately from the MiSeqDx instrument is limited to users with a MiSeqDx.

This software includes Illumina User Management Software, Illumina Worklist Manager, and MiSeq Reporter v2.2.31.1. Download and complete the form and return to to receive access to this 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. This version of Sequencing Analysis Viewer (SAV) is compatible with data from MiniSeq, MiSeq (with MCS v2.6.2 and higher), NextSeq, HiScanSQ, all HiSeq systems, and NovaSeq.

Download and unzip this file to install SAV for viewing sequencing runs on an offline computer. This SAV version requires Windows.NET Framework 4.5.1 and Visual C Redistributable for Visual Studio 2015. If your system is using Windows.NET Framework 4 or you are running a MiSeq with MiSeq Control Software v2.5 and lower, continue using SAV 1.8.37.

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

The bed file can be loaded into UCSC Genome Browser to visualize targeted regions or to compare with other data of interest accessible via UCSC Browser's tables function. The file includes chromosome, targeted coordinates and the gene symbol concatenated the chr-start-stop information. Note regarding biomarker patents and other patents unique to specific uses of products. Many Illumina products can be used to analyze a sample and detect the presence or absence of specific genomic variants within or across genes, nucleic acid sequences or genomic regions, some of which, and their use in specific applications, may be protected by patents.

Customers are advised to determine whether they are required to obtain licenses from the party that owns or controls such patents in order to use the product in the customer’s specific application. Illumina no longer accepts orders for TruSight Cardiomyopathy. The recommended replacement product is the.

Illumina remains committed to providing you with high-quality support and service. This download contains an update to the Genome Analyzer�s sequencing control and real-time analysis software (SCS2.9/RTA1.9).

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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 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. '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.'

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).

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

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This package is customer installable, but review the installation notes to make sure that your system meets the requirements for this update. 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. This download contains the Nextera Rapid Capture Exome v1.2 release notes, targeted regions manifest files (.txt and.bed), and the exome probe manifest. The readme document describes the Nextera Rapid Capture Exome v1.2 manifest files.

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The targeted regions manifest files list the 214,126 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19. The Nextera Rapid Capture Exome v1.2 Targeted Regions Manifest and the Nextera Rapid Capture Exome Probe Manifest files are in.txt format. This format is required by the HiSeq Analysis Software. Innovative technologies At Illumina, our goal is to apply innovative technologies to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. It is mission critical for us to deliver innovative, flexible, and scalable solutions to meet the needs of our customers.

As a global company that places high value on collaborative interactions, rapid delivery of solutions, and providing the highest level of quality, we strive to meet this challenge. Illumina innovative sequencing and array technologies are fueling groundbreaking advancements in life science research, translational and consumer genomics, and molecular diagnostics. For Research Use Only. Not for use in diagnostic procedures (except as specifically noted). © 2018 Illumina, Inc.

All rights reserved. All trademarks are the property of Illumina, Inc. Or their respective owners. For specific trademark information, see.