TCB No September Technical Bulletin. GS FLX+ System & GS FLX System. Installation of 454 Sequencing System Software v2.

Transcription

1 TCB No September 2012 Technical Bulletin GS FLX+ System & GS FLX System Installation of 454 Sequencing System Software v2.8 Summary This document describes how to upgrade the 454 Sequencing System Software to Version 2.8 on offinstrument computers. This includes the GS FLX+ Computing Station and the GS FLX Titanium Cluster. While specific instructions are provided only for Roche-supplied computing solutions, they are generally applicable to any custom datarig or cluster environment, provided it is running a supported version of the Linux Operating System. The 454 Sequencing System Software Version 2.8 (P/N ) consists of six disks: 1. GS FLX+ or GS FLX System Data Acquisition Disk, v2.8 - includes the Genome Sequencer FLX Instrument Control Software and GS FLX+ Instrument Control Software (not addressed in this document, as it is for Instruments only, not datarigs or clusters). 2. GS FLX+ or GS FLX System Data Processing Disk, v2.8 - includes the GS Run Processor Suite, the GS Support Tool and the GS Run Browser. 3. GS FLX+ or GS FLX System Data Analysis Disk, v2.8 - includes the GS De Novo Assembler, the GS Reference Mapper and the GS Amplicon Variant Analyzer applications. 4. GS FLX+ or GS FLX System Documentation Disk, v2.8 includes the e-help files, which are a version of the 454 Sequencing System Software Manual, v 2.8, that can be invoked from the Help buttons in the various software applications. Page 1 of 26

2 5. GS FLX+ or GS FLX System GS GType Assay Software Add-on, v2.1 - for use only in conjunction with the GS GType HLA Assay or the GS GType Leukemia Assays (not addressed in this document. Please refer to TCB No , Installation of GS GType Assay Software Add-On v2.1 ). 6. GS FLX+ or GS FLX System Test Data Set - includes a small test dataset, used for testing the success of software installation. This document first describes the software changes between versions 2.7 and 2.8. The document then describes how to perform the version 2.8 software upgrade on any off-instrument datarig (whether provided by Roche, or completely custom). Information about GS GType Assay Software Add-on With every new version of 454 Sequencing System Software, including v2.8, a new version of GS GType Assay Software Add-on is released to support it. If you have previously installed GS GType HLA Software Add-on (Version 1.0, 1.1, or 2.0), then once the 454 Sequencing System Software is upgraded to Version 2.8, you will need to install the most recent version of the GS GType Assay Software Add-on. GS GType Assay Software Add-on v2.1 is bundled as part of the 454 Sequencing System Software Version 2.8 disk set. If you are a user of the GS GType HLA Assay or the GS GType Leukemia Assays, please refer to TCB No , Installation of GS GType Assay Software Add-On v2.1, available from for information on how to install the Add-on software. If a newer version than 2.1 of the GS GType Assay Software Add-on is available, use that version instead (new versions of the Add-on software are always backwards compatible). Note: If you encounter issues or errors during the upgrade procedures not described in this document, please contact your Roche customer service representative for assistance. Page 2 of 26

3 Table of Contents Summary 1 Information about GS GType Assay Software Add-on 2 Version History of this Document 4 Changes in 454 Sequencing System Software Version Data Acquisition 4 Data Processing 4 Data Analysis 5 Units Concerned 5 Pre-Installation Activities 5 Back Up Your Data Prior To Upgrade 5 Supported Operating Systems 5 Root Password 6 Obtaining the Software 6 Extracting the 454 Sequencing System Software Distribution Files 7 How to Upgrade a Datarig or Cluster to 454 Sequencing System Software Version Upgrading to the 454 Sequencing System Data Processing Package, v Upgrading to the 454 Sequencing System Data Analysis Package, v Upgrading to the 454 Sequencing System Documentation Package, v Special Considerations for Cluster Installs 23 Updating the Support Utilities on the GS FLX Titanium Cluster 23 Custom Clusters 24 Post-Installation Activities 25 GS GType Assay Software Add-on 25 For life science research only. Not for use in diagnostic procedures. Page 3 of 26

4 Version History of this Document Version # Changes 01 a. New document. Changes in 454 Sequencing System Software Version 2.8 Version 2.8 incorporates a large number of corrections and new features. As the software is shared with the GS Junior System, many of these changes have been described previously. Refer to TCB , Installation of 454 Sequencing System Software v2.6, and TCB , Installation of 454 Sequencing System Software v2.7 and Service Patch 1, available on Additional features and updates for Version 2.8 are presented below. For complete documentation of the software, refer to the 454 Sequencing System Software Manual, V2.8. Data Acquisition Additional run script provided for XL+ sequencing. Users can choose between flow pattern A (cyclic) and flow pattern B (acyclic). Refer to 454 Sequencing System Software Manual, v 2.8 for more information. Reorganization of I/O processes, reducing the burden on the I/O and networking OS subsystems on the instrument server. These changes lower the frequency of image loss events. Data Processing Signal processing on 32-bit architectures is not supported for acyclic (flow pattern B) runs. Image processing of acyclic runs is allowed on 32-bit machines (e.g.,the GS FLX or GS FLX+ server). Full processing of cyclic runs is still supported on 32-bit machines. Adjustment of several existing image and signal processing algorithms to accommodate acyclic flow patterns. Replacement of the nucvalveeventbalancer module with the new flowbalancer module for correcting flow events in acyclic runs. New quality filter parameter: qualityminlength. Sets the minimum allowable flow length for all passing reads that are trimmed for quality. Default value is 112 flows for acyclic runs, -1 for all other runs. Refer to 454 Sequencing System Software Manual, v 2.8 for more information. Improvements to the globaldroopcorrection module, an algorithm specific to the Shotgun pipeline. Reduces rare occurences of G-overscaling towards the end of a run. Corrections in GS Support Tool so that all log files are now properly collected. option removed from GS Support Tool. Network transfers of GS Support Tool output is now ftp-only. Known issue: GS Support Tool fails to recognize path names containing spaces. Workaround: do not put spaces in directory names. Known issue: Occasional pipeline crashes on the GS FLX Titanium Cluster. More details provided later in this document (see below). Known issue: The version of the openmpi library used v2.8 fails to function properly on certain custom clusters. More details provided later in this document (see below). Page 4 of 26

5 Data Analysis Adjustment of flowgram views to support acyclic flow patterns. Improvements to fusion detection algorithms and addition of two new files to GS Reference Mapper output: 454AllVariantFusionTable.txt and 454HCVariantFusionTable.txt. Resolved issue: The Include filter file: file specification box on the Input sub-tab of the Parameters tab now works properly. Resolved issue: The Multiplex column of the GS Reads sub-tab of the Project tab no longer fails to show a comma-delimited list of the MIDs that were included in the project. Known Issue: High-depth cdna projects may take significantly longer to compute than with previous versions of the software, and possibly not complete at all. The workaround is to use Version 2.6 of the GS Reference Mapper or GS De Novo Assembler. Known Issue: The Add MID function in the Configure wizard of a Multiplex project doesn't allow editing of the custom MID name. Known Issue: The Summary Results tab of any Multiplex project fails to appear when selected. The workaround is to directly refer to the text files for the summary information, and not to select that tab. Units Concerned This document describes the upgrade procedure for off-instrument datarigs and clusters only. 454 Sequencing System Software Version 2.8 is not a customer-installable release. Therefore only qualified Roche personnel should upgrade a GS FLX or GS FLX+ Sequencer. Pre-Installation Activities Back Up Your Data Prior To Upgrade Caution: Any change to the system, including this upgrade, comes with a risk of data loss. Prior to performing the following upgrade instructions, be sure to back up all data from the computer to a safe location. Typical options would include either a USB-connected hard disk drive, or a remote network location. Supported Operating Systems 454 Sequencing System Software, v2.8 is installable only on the Linux operating system. Many different distributions are available for off-instrument custom datarigs and clusters, however not all are supported. 454 Sequencing System Software, v2.8 is fully tested and supported on the following linux OS distributions: Red Hat Enterprise Linux (RHEL), v4.3 (32-bit) CentOS, v5.4 and v5.5 (64-bit) Fedora Core (FC), v4 (64-bit) Page 5 of 26

6 A wider range of linux OS distributions are expected to be compatible with 454 Sequencing System Software, v2.8 although not all of them have been tested: RHEL, v4.3 through v6.x (32-bit and 64-bit) CentOS, v4.3 through v6.x (32-bit and 64-bit) FC, v4 through v16 (32-bit and 64-bit) OpenSUSE, v10 through v11 (32-bit and 64-bit) If you experience problems with the installation on any of the above listed distributions, contact a Roche Customer Support representative for assistance. All other linux distributions are not expected to be compatible, and are not supported. Root Password The root password for your datarig or cluster may be required for the upgrade procedure. Before starting the procedure, be sure to have to root password available. If you do not know the root password, contact your local IT support or linux administrator for assistance. Do not proceed until you have the root password. Obtaining the Software Your Roche representative can provide you with the set of six disks which together constitute the 454 Sequencing System Software v2.8 (Part number ). The complete set of six disks is not required for a full installation of Version 2.8 Software on a datarig or cluster. Only Disk 2 (Data Processing), Disk 3 (Data Analysis) and Disk 4 (Documentation) are necessary. Disk 5 (Add-on) is only required if you are a user of the GS GType HLA Assay or the GS GType Leukemia Assays. Please refer to TCB No , Installation of GS GType Assay Software Add-On v2.1, available from to install the Add-on software. Disk 6 (Test Data Set) is used at the end to verify correct installation, but any known good pre-existing dataset available on the datarig or cluster will suffice. You may also be able to obtain the Software distribution files indicated below from a Roche FTP site. If available, your Roche representative can provide you with the necessary download information. Each package is provided as its own individual distribution file: DataProcessing_2.8_All.tgz DataAnalysis_2.8_All.tgz Documentation_2.8_All.tgz Addons_2.1_All.tgz Page 6 of 26

7 Note: Disk 1, GS FLX+ or GS FLX System Data Acquisition Disk, v2.8, is not installed on datarigs or clusters. It is an Instrument-only software package. Since upgrading the GS FLX or GS FLX+ Sequencer to Version 2.8 is not a customer-installable procedure, the Data Acquisition package is not available for download. Note: Disk 6, GS FLX+ or GS FLX System Test Data Set, is too large for downloading. Disk 6 is available only with the physical disk set. It is not an essential component of the software. Any pre-existing sequencing run can be used to test the correct installation of the Data Processing software on the datarig or cluster. Note: A tarball is a linux/unix compressed archive file (similar to a zip file). A group of files is first archived with tar, then compressed with gzip files have a.tgz file extension. For owners of the GS FLX Titanium Cluster, an additional file is required: 454SupportUtils_2.8.tgz This tarball contains two scripts (clustersupporttool.sh and valtool.sh) and a configuration file (gsticluster.sh) that are specific to the GS FLX Titanium Cluster. Extracting the 454 Sequencing System Software Distribution Files When connected to the internet, the datarig or cluster can be used to directly download the 454 Sequencing System Software v2.8 distribution files. Any other computer can also be used for downloading. The distribution files can be transferred to datarig or cluster via a USB memory stick (USB Storage), or transferred over an internal network. Caution: When obtaining the distribution files via FTP, be sure to transfer the files in binary mode, otherwise the files will be corrupted during downloading. In addition, Do not unpack, unzip, or untar the distribution files prior to the step calling for this action (see below). Software distribution files are created in a specific manner, which preserves the correct Linux file permissions for each file in the tarball archives. If these files are expanded and copied to a media, such as a CD-ROM or a USB device, outside of the installation environment or on another operating system, the file permissions might be changed when extracted. These changes could create downstream problems or errors during installation. Note: The following instructions pertain to installation on a GS FLX+ Computing Station. The installation process (i.e., running the Setup Wizard) should be similar regardless of the datarig or cluster. Specific details of the various operations taking place outside of the installer may however vary. Page 7 of 26

8 If the software distribution files were transferred via USB, insert the USB storage device into the USB port and wait for the system to detect the USB storage device and automatically mount it. 1) Copy the distribution files to a standard location, such as /home/adminrig/downloads, (used in the example). 2) For each of the tarballs, perform steps 2 through 6 to extract the contents into its own folder. Double-click on the tarball to open the Archive Manager, as shown here: 3) Click the Extract button to open the Extract dialog box, as shown here: Page 8 of 26

9 4) Click Extract again to extract the contents of the tarball into a new folder that will be automatically created, as shown here for the Data Processing tarball: Page 9 of 26

10 5) Click Archive -> Close, or click the Close box, to close the Archive Manager window. 6) Double-click on the newly created folder to open it and reveal the setup.sh icon for the package (except for 454SupportUtils_2.8, which does not have a setup.sh icon). For each package, follow the installation directions as detailed individually in the next sections. How to Upgrade a Datarig or Cluster to 454 Sequencing System Software Version 2.8 The upgrade procedure for datarigs and clusters includes the installation of the 454 Sequencing System Data Processing Software v2.8, followed by the installation of the 454 Sequencing System Data Analysis Software v2.8 and 454 Sequencing System Documentation v2.8. For the GS FLX Titanium Cluster, the Support Utilities (454SupportUtils_2.8) must also be upgraded. Note: Although 454 Sequencing System Software v2.8 uses graphical installers, a pseudo text mode is automatically used when installing from a terminal session where X forwarding is not available. X forwarding for the session must be turned off for this to work automatically. If X forwarding is turned on and you do not have local X server, the installer will not launch. The following instructions in this TCB assume a GNOME windowing environment, the default on the GS FLX+ Computing Station, as opposed to, for example, KDE, which is the default on the Genome Sequencer FLX Instrument. In all cases, the installation/upgrade process is identical. Specific screenshots and operations may however be slightly different depending on your environment. Page 10 of 26

11 Upgrading to the 454 Sequencing System Data Processing Package, v2.8 Note: These installation instructions assume the software distribution files were copied to the /home/adminrig/downloads directory on the cluster or datarig. They are also applicable when files were copied to a different location, although the screenshots may differ slightly. 1. Wait until all data processing and data analysis has been completed. Do not perform the upgrade while any 454 software is running. 2. If installation is performed directly from the CDs, insert the 454 Sequencing System Data Processing Disk, v2.8 into the optical drive. Wait for the system to detect the CD, automatically mount it, and open it to reveal a folder containing the setup.sh icon. Otherwise, the setup.sh icon will be present as a result of following the instructions in the earlier section Extracting 454 Sequencing System Software Distribution files. Note that the window titles will be slightly different between a CD-based vs. tarball-based installation. In addition, the CD-based installation will have a file called RPM-GPG-KEY that the tarballbased distribution does not have (this is unimportant, as you will not use this file). Start the installation procedure by double-clicking the setup.sh icon: 3. You will be prompted for what to do; click Run to proceed: Page 11 of 26

12 4. Two windows will open. The text-based window will run in the background and requires no interaction until the end of the install procedure: 5. The other window is the Setup Wizard that requires user interaction. Click the Next button on the two initial screens of the Setup Wizard: 6. You will then be presented with a choice between System and Local installation mode. Note: The system-wide installation under root privileges grants access to software version 2.8 to all users who have access to the machine, and the default installation path would be /opt/454. The local installation under user adminrig limits access to software version 2.8 to the user adminrig, and the default installation path will be /home/adminrig/454. Page 12 of 26

13 Select System as the install type, and click Next to proceed: 7. At the Checking Environment step you will be prompted to continue the upgrade. Click the Yes button to continue: 8. At the next screen, click Next to continue: Page 13 of 26

14 9. If the account you are using does not have sudo privileges, you will be prompted to provide the root password. If so, type it in and click OK. Otherwise proceed to the next step. 10. Take note of the location of the installation log file for future reference, which is presented both at the top and at the bottom of the output window. When prompted, click the Next to continue: 11. If you were upgrading from a previous installation, then the installer will detect and save any files that may have been customized for your installation, such as custom pipeline xml files. Take note of the location of any such files, as you will need them in order to make similar customizations to the upgraded Version 2.8 pipeline files. When prompted, click the Finish button, and the Setup Wizard will close: Page 14 of 26

15 12. Return to the text-based window and hit the Enter key to dismiss it, as prompted: 13. This concludes the procedure for upgrading to the 454 Sequencing System Data Processing Package, v2.8. If installing from the CD, eject the disk at this time. Proceed to the next section, Upgrading to the 454 Sequencing System Data Analysis Package, v2.8. Upgrading to the 454 Sequencing System Data Analysis Package, v Wait until all data processing and data analysis has been completed. Do not perform the upgrade while any 454 software is running. 2. If installation is performed directly from the CDs, insert the 454 Sequencing System Data Analysis Disk, v2.8 into the optical drive. Wait for the system to detect the CD, automatically mount it, and open it to reveal a folder containing the setup.sh icon. Otherwise, the setup.sh icon will be present as a result of following the instructions in the earlier section Extracting 454 Sequencing System Software Distribution files. Note that the window titles will be slightly different between a CD-based vs. tarball-based installation. In addition, the CD-based installation will have a file called RPM-GPG-KEY that the tarball-based distribution does not have (this is unimportant, as you will not use this file). Start the installation procedure by double-clicking the setup.sh icon: Page 15 of 26

16 3. You will be prompted for what to do; click Run to proceed: 4. Two windows will open. The text-based window will run in the background and requires no interaction until the end of the install procedure: 5. The other window is the Setup Wizard that requires user interaction. Click the Next button on the two initial screens of the Setup Wizard: 6. You will then be presented with a choice between System and Local installation mode. Note: The system-wide installation under root privileges grants access to software version 2.8 to all users who have access to the machine, and the default installation path would be /opt/454. The local installation under user adminrig limits access to software version 2.8 to the user adminrig, and the default installation path will be /home/adminrig/454. Page 16 of 26

17 Select System as the install type, and click Next to proceed: 7. At the Checking Environment step you will be prompted to continue the upgrade. Click the Yes button to continue: 8. At the next screen, click Next to continue: Page 17 of 26

18 9. If the account you are using does not have sudo privileges, you will be prompted to provide the root password. If so, type it in and click OK. Otherwise proceed to the next step. 10. Take note of the location of the installation log file for future reference, which is presented both at the top and at the bottom of the output window. When prompted, click the Finish button, and the Setup Wizard will close: 11. Return to the text-based window and hit the Enter key to dismiss it, as prompted: 12. This concludes the procedure for upgrading to the 454 Sequencing System Data Analysis Package, v2.8. If installing from the CD, eject the disk at this time. Proceed to the next section, Upgrading to the 454 Sequencing System Documentation Package, v2.8. Page 18 of 26

19 Upgrading to the 454 Sequencing System Documentation Package, v Wait until all data processing and data analysis has been completed. Do not perform the upgrade while any 454 software is running. 2. If installation is performed directly from the CDs, insert the 454 Sequencing System Documentation Disk, v2.8 into the optical drive. Wait for the system to detect the CD, automatically mount it, and open it to reveal a folder containing the setup.sh icon. Otherwise, the setup.sh icon will be present as a result of following the instructions in the earlier section Extracting 454 Sequencing System Software Distribution files. Note that the window titles will be slightly different between a CD-based vs. tarball-based installation. In addition, the CD-based installation will have a file called RPM-GPG-KEY that the tarballbased distribution does not have (this is unimportant, as you will not use this file). Start the installation procedure by double-clicking the setup.sh icon: 3. You will be prompted for what to do; click Run to proceed: Page 19 of 26

20 4. Two windows will open. The text-based window will run in the background and requires no interaction until the end of the install procedure: 5. The other window is the Setup Wizard that requires user interaction. Click the Next button to proceed: 6. You will then be presented with a choice between System and Local installation mode. Note: The system-wide installation under root privileges grants access to software version 2.8 to all users who have access to the machine, and the default installation path would be /opt/454. The local installation under user adminrig limits access to software version 2.8 to the user adminrig, and the default installation path will be /home/adminrig/454. Page 20 of 26

21 Select System as the install type, and click Next to proceed: 7. At the Checking Environment step you will be prompted to continue the upgrade. Click the Yes button to continue: 8. At the next screen, click Next to continue: Page 21 of 26

22 9. If the account you are using does not have sudo privileges, you will be prompted to provide the root password. If so, type it in and click OK. Otherwise proceed to the next step. 10. Take note of the location of the installation log file for future reference, which is presented both at the top and at the bottom of the output window. When prompted, click the Finish button, and the Setup Wizard will close: 11. Return to the text-based window and hit the Enter key to dismiss it, as prompted: 12. This concludes the procedure for upgrading to the 454 Sequencing System Documentation Package, v2.8. If installing from the CD, eject the disk at this time. Page 22 of 26

23 This concludes the software installation procedure for datarigs. You can verify successful installation by launching any of the applications (GS RunBrowser, GS De Novo Assembler, etc.) and clicking the About button. For example: If your system does not support placement of Desktop icons (or you did a local install) you can verify the version by typing, for example, runassembly --version on the command line. To confirm the successful installation of the pipeline, perform run processing on either the GS FLX+ or GS FLX System Test Data Set or any other dataset known to have been successfully processed by a previous version of the software. Special Considerations for Cluster Installs Updating the Support Utilities on the GS FLX Titanium Cluster The support utilities are comprised of three scripts, valtool.sh, clustersupporttool.sh and gsticluster.sh. The valtool.sh performs a short series of non-invasive tests to determine the fitness of the cluster for running the analysis pipeline software. At the completion of the tests, simple PASS/FAIL/UNTESTED results will be shown on screen. A detailed log file will be output to valoutput.txt in the user's home directory. clustersupporttool.sh collects all the system information about the cluster and displays the results on screen. The gsticluster.sh configures the GS FLX Titanium Cluster environment variables. Download the tarball to /home/adminrig of the GS FLX Titanium Cluster, and extract it there: tar zxvf /home/adminrig/454supportutils_2.8.tar.gz (Enter) Page 23 of 26

24 The output should give: 454SupportUtils_2.8/ 454SupportUtils_2.8/454utils_checksum.txt 454SupportUtils_2.8/clusterSupportTool.sh 454SupportUtils_2.8/gsTiCluster.sh 454SupportUtils_2.8/valTool.sh Go into the 454SupportUtils_2.8 folder and check the md5sum: cd /home/adminrig/454supportutils_2.8 (Enter) md5sum c 454utils_checksum.txt (Enter) The output should give: clustersupporttool.sh: OK gsticluster.sh: OK valtool.sh: OK If the integrity check is OK, update the Support Utilities. First update the current version of the valtool.sh by typing: cp valtool.sh /home/adminrig (Enter) Update the current version of the clustersupporttool.sh by typing: cp clustersupporttool.sh /home/adminrig (Enter) Update the current version of the gsticluster.sh by typing: sudo cp gsticluster.sh /etc/profile.d (Enter) This completes the installation of the Support Utilities. Custom Clusters 454 Sequencing System Software Version 2.8 will run on a variety of systems, including custom clusters that Roche does not fully support due to every such system essentially being unique. Typically sites running custom clusters have the local IT and linux administrative expertise to properly set up, configure, and run their clusters, as well as install and run the 454 Software. With Version 2.8 of the 454 Sequencing System Software, the version of the Open MPI library that ships with the Software has changed from version to version The Open MPI library is the software component that allows parallel processing jobs to spawn on the individual nodes of a cluster. Version of Open MPI has an issue that may prevent jobs from correctly spawning on certain clusters. This is not an issue with the GS FLX Titanium Cluster, but it has been observed on custom Page 24 of 26

25 clusters running the Sun Grid Engine. It is not known if this issue is limited to SGE clusters, or if it is a more general problem. If you have previously successfully set up and configured 454 Sequencing System Software Version 2.6 on your custom cluster, and therefore know that your cluster and the 454 software are correctly configured and working, yet you are unable to get 454 Sequencing System Software Version 2.8 to execute in the same way, then we recommend the following workarounds. If jobs are not being spawned across nodes of the cluster and you have configured the cluster to use tight integration, then add the mpirun options for number of slots and list of machines to your $GS_MPIARGS (or $GS_MPIARGS_COMMAND, depending on your configuration) environment variable. If you use rshd for spawning jobs across machines and incur a key verification failure error message when running a job, add the following string to your $GS_MPIARGS or $GS_MPIARGS_COMMAND environment variable: -mca plm ^rshd Finally, if you find high NFS traffic to the head node (or wherever the run directory is located) during run processing, add the following string to your $GS_MPIARGS or $GS_MPIARGS_COMMAND environment variable: -x GS_CACHEDIR=$GS_CACHEDIR where $GS_CACHEDIR should give the path to a local disk found on each node of the cluster, so that the processing code can utilize local disks for scratch space, avoiding the high NFS traffic. If these workarounds fail to resolve the issue, contact a Roche Customer Support representative. The issue will then be escalated to a cluster expert within Roche. Post-Installation Activities GS GType Assay Software Add-on If you previously installed the GS GType Assay Software Add-on (or GS GType HLA Software Addon), you must upgrade to the current version of the Add-on after the Version 2.8 upgrade is complete. At the time of this writing, the current version of GS GType Assay Software Add-on is 2.1. Refer to TCB No , Installation of GS GType Assay Software Add-On v2.1 (available from for information on how to install the Add-on software. Page 25 of 26

26 For life science research only. Not for use in diagnostic procedures. License disclaimer information is subject to change or amendment. For current license information on license disclaimers for a particular product, please refer to 454, 454 LIFE SCIENCES, 454 SEQUENCING, GS FLX, GS FLX+, GS GTYPE, and GS JUNIOR are trademarks of Roche All other product names or trademarks are property of their respective owners. Page 26 of 26