Next-Generation Sequencing Installer

With the advent of Next Generation sequencing, several new external alignment algorithms have been integrated in Sequencher to align the large quantity of data produced by Next Generation sequencing machines. These algorithms, Maq and GSNAP, join Clustal (the first external algorithm to be added to Sequencher). The Maq and GSNAP algorithms were written to run on Unix-based systems. Mac OS X is a Unix-based operating system. Windows, on the other hand, will need to have Cygwin, a Unix emulation environment, installed in order to run the alignment tools. To take full advantage of these tools, you will also need to install Tablet—a third-party graphical viewer.

The instructions which follow show you how to use the all-in-one installers which will place almost everything you need to run these algorithms on your computer.  The Tablet viewer is a separate installer but only takes moments to install. For more information on installing and using the external alignment algorithms in Sequencher, please refer to the Using External Tools with Sequencher tutorial.

Quick and Easy Set Up for NGS Aligners

INSTALLING MAQ AND GSNAP ON WINDOWS

The Windows self-extracting installer will place Cygwin, Maq, Maqview, and GSNAP and their related files where they need to be in order to work with Sequencher.

1. Download ExternalToolsInstallerV1.zip.
2. Double-click on the ZIP archive to open it. A window will open containing ExternalToolsInstallerV1.exe as well as src and Tablet folder. 
3. Double-click on the ExternalToolsInstallerV1.exe and click the Extract all button. Accept the default settings provided by Windows for extracting all the files.
4. Double-click on the newly extracted ExternalToolsInstallerV1.exe file to start the installation process. A dialog will open asking for the location to Extract to:
   

   

5. You should see a path very much like the one in the picture above. Do not accept this default path. Sequencher requires these files extracted directly to the root of your drive. Delete everything past the first \ character.  In most cases, your root drive location will be C:\ but you may have a different drive letter.
6. Click on the Extract button to continue.
7. A new window appears which shows the progress of the installer. When the screen disappears, the installation is complete and Maq and GSNAP are ready for use in Sequencher.

INSTALLING THE TABLET VIEWER ON WINDOWS

To install the Tablet viewer on your computer, follow these steps:

1. Open the Tablet folder. There are two installers. The tablet_windows_x64_1_11_05_03 installer is for 64-bit systems
   and the tablet_windows_x86_1_11_05_03 installer is for 32-bit systems.
2. Tablet requires administrator privileges in order to install. If you are an Administrator user, double-click on the correct
   Tablet installer for your operating system. If you are a Standard user, right-click on the correct Tablet installer for your
   operating system and select ‘Run as administrator’.
3. If you are presented with a dialog with a Run button on it, click on the Run button to continue.
4. A new window appears informing you that the installer is preparing the wizard to guide you through the setup.
5. The Tablet Setup Wizard dialog appears next.  Click on the Next button on that dialog.
6. An installer license agreement window appears next.  Accept the License Agreement and again click on the Next button.
7. You will be prompted for a destination location for the installation. The default location is Programs Files\Tablet.  Don’t change this location and click on the Next button.
8. You will be asked whether you want to create a Start Menu folder and create a shortcut. If you wish you may uncheck these checkboxes. Now click on the Next button to continue with the installation.
9. A final window appears informing you that the Setup has finished. Uncheck the Run Tablet checkbox and click on the Finish button. Tablet is now ready for use in Sequencher.

INSTALLING MAQ AND GSNAP ON MAC OS X

You must be an Administrator or have an administrator’s password in order to install the external tools on Mac. The Mac OS X installer will place Maq, Maqview, GSNAP, and their related files where they need to be in order to work with Sequencher.

1. Download ExternalToolsInstallerV1.dmg.
2. Double-click on the downloaded dmg file.
3. Double-click on the new volume icon named ‘External Tools Installer V1’ to open it.
4. Double-click on either the 32-bit or 64-bit installer package to begin installation. (Don’t worry about choosing the wrong one—the installation will only proceed if it matches your machine.)
5. A welcome window will appear and you will be guided through the installation. Click on the Continue button.
6. An information screen appears telling you how much space is required for the installation.  Click on the Install button.
7. You will be asked for your password.  One is required in order to allow changes to be made to your system. Type in the password and click on the OK button.

The installer starts. You will see various status messages as the files are written to your system. Finally, a screen appears telling you that everything was installed successfully. Click on the Close button. The external tools Maq and GSNAP are now ready for use in Sequencher.

8. Eject the disk image icon from your desktop unless you are planning to install the Tablet viewer next.

INSTALLING THE TABLET VIEWER ON MAC OS X

To install the Tablet viewer on your computer, follow these steps:

1. By default, Tablet will install in the Applications folder and that is where Sequencher expects to find it. Because installing in the Applications folder requires administrator privileges, you must be an administrator to install.
2. Double-click on the Tablet folder icon to open the folder.
3. Double-click on the tablet_macos dmg file to open the installer.
4. Double-click on the Tablet Installer to start the installation.
5. A Welcome screen will appear.  Click on the Next button.
6. An installer license agreement window appears next.  Accept the License Agreement and again click on the Next button.
7. You are prompted for a destination location for the installation. The default location is Applications. Don’t change this location.  Next click on the Next button.
8. A final window appears informing you that the Setup has finished. Uncheck the Run Tablet checkbox and click on the Finish button. Tablet is now ready for use in Sequencher.
9. Eject the disk image icon from your desktop.