Next-Generation Sequencing Installer

Quick and Easy Set Up for NGS Aligners and Assemblers

Installing External Applications on Windows

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

Download ExternalToolsInstallerV3.zip
Extract/unzip the archive and open the installer folder. It will contain ExternalToolsInstaller.exe, ClustalW2, src, and Tablet folders, and a License.txt file.
Double-click on ExternalToolsInstaller.exe. Accept the installation defaults including the license agreement terms.
A new window appears which shows the progress of the installer. When the installation is complete, GSNAP, Maq, Maqview, MUSCLE, and Velvet are ready for use in Sequencher.

Installing the Tablet Viewer on Windows

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

Open the Tablet folder. There are two installers. The tablet_windows_x64_1_12_03_26 installer is for 64-bit systems and the tablet_windows_x86_1_12_03_26 installer is for 32-bit systems.
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’.
If you are presented with a dialog with a Run button on it, click on the Run button to continue.
Accept all of the installation defaults. You will be prompted for a destination location for the installation. The default location is Program Files\Tablet. Don’t change this location.

Installing Clustal on Windows

To install Clustal on your computer, follow these steps:

Open the ClustalW2 folder.
Clustal requires administrator privileges in order to install it. If you are an Administrator user, double-click on the Clustal installer. If you are a Standard user, right-click on the Clustal installer and select ‘Run as administrator’.
Accept all of the installation defaults. You will be prompted for a destination location for the installation. The default location is Program Files\ClustalW2 for 32-bit systems or Program Files (x86)\ClustalW2 for 64-bit systems. Don’t change this location.

Installing External Applications 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 GSNAP, Maq, Maqview, MUSCLE, Velvet, and their related files where they need to be in order to work with Sequencher.

Download ExternalToolsInstallerV3.dmg
Double-click on the downloaded dmg file.
Double-click on the new volume icon named ‘External Tools Installers’ to open it if it doesn’t open automatically.
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.)
A welcome window will appear and you will be guided through the installation. Click on the Continue button.
A license agreement window will appear. Click on the Continue button and then on the Agree button.
An information screen appears telling you how much space is required for the installation. Click on the Install button.
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 Install Software 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 GSNAP, Maq, Maqview, MUSCLE, and Velvet are now ready for use in Sequencher.
Eject the disk image icon from your desktop unless you are planning to install Clustal or the Tablet viewer next.

Installing the Tablet Viewer on Mac OS X

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

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.
Double-click on the Other Installers folder icon to open the folder.
If you are on Mountain Lion, change the security setting for ‘Allow applications downloaded from:’ to Anywhere.
Double-click on the tablet.dmg file to open the installer.
Double-click on the Tablet Installer to start the installation.
Accept all of the installation defaults. You are prompted for a destination location for the installation. The default location is Applications. Don’t change this location.
Eject the disk image icon from your desktop.
If you are on Mountain Lion and you changed the ‘Allow applications downloaded from:’ security setting to Anywhere, change it back to ‘Mac App Store and identified developers’.

Install Clustal on Mac OS X

To install Clustal on your computer, follow these steps:

By default, Clustalw2 needs to be in the Applications folder and that is where Sequencher expects to find it.
Double-click on the Other Installers folder icon to open the folder.
Double-click on the clustalw2.dmg file.
Double-click on the clustalw-2.1-macosx folder to open the folder.
Drag the clustalw2 application to the Applications folder on your Macintosh Hard Drive.
If you are on Mountain Lion, double-click on the clustalw2 application to run it once.

Questions

We would love to hear from you! Please give us a call at 734-769-7249 or fill out our contact form here.

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"Sequencher is not just the best sequence analysis program I have used; it is one of the best pieces of software I have used. Period. It is intuitive; it does exactly what I want it to do in pretty much the way I would expect it to work. "

Wilson Clements, Ph.D., University of California, San Diego

"I am very satisfied with how sequencher handles heterozygous calls in autosomal sequencing and potential heteroplasmies in mitochondrial resequencing. I found the forensics addon package for the general forensics community to be very helpful! "

Eric Wang, Ph.D Statistical Geneticist, Algorithm Development and Data Analysis Affymetrix, Inc.

"I just wanted to let you know how much the modifications to Sequencher have assisted in our data flow. The time saving has been amazing. Assembling our data has taken third the time it usually does, and has allowed for the smoothest assembly of our data for a vaccine selection that I can remember. Additionally noteworthy as we have produced more data for this selection than ever before. Please let your programmers know that the work that they have done has truly helped and thank them for their efforts. "

An Associate Research Fellow, US Centers for Disease Control and Prevention

"After using Sequencher for years as a grad student, I was forced to switch to MacVector as a postdoc in a new lab. Sequencher is so much easier to use than MacVector and has such a superior interface that I used the demo version of Sequencher for months rather than the lab copy of MacVector. Sequencher feels as though it is written by biologists that can write software, rather than programmers attempting to write biological software. Any life scientist who has spent time pulling their hair out over non-intuitive software will greatly appreciate this distinction. "

Dave Parker, University Of Michigan Cell And Developmental Biology

"I am involved in resequencing projects for disease association studies. Sequencher was of tremendous help to me in these projects for- discovery of SNPs, detection of known SNPs, intronic/exonic SNPs & amino acid changing SNPs. I have been using it for sequence analysis of ABI data files since 2000. It is easy to operate and user friendly. It was a pleasure to be involved in the beta test program for version 4.6. What I liked in this new version is assembly function & variance table. Assemble to reference by defining assembly parameters using advance expression feature is very useful, it saves a lot of time and sequences can be assembled by defining feature of your choice e.g. sample ID, primer ID, or well position etc. Technical Support group at the Gene Codes Corporation has been very receptive to the idea of introducing variance table. With this feature it is now possible to export genotypes. Using this feature I am not only able to export whole table but also selected few columns using “export selected” option button. "

Manjula Maheshwari, Human Genome Sequencing Center Baylor College of Medicine Houston, Texas

"Whether it has been for building contigs in the search for novel causative mutations, verifying proper vector construction, or simply aligning large numbers of samples for typing of a single SNP, it has been an invaluable tool. With the advent of next generation sequencing technologies, it becomes even more necessary to have trustworthy, user-friendly software. "

Rob Loechel, Chief Scientific Officer, Vetgen, L.L.C.

"Sequencher, from Gene Codes of Ann Arbor, Mich., is possibly today's most popular software for DNA Sequencing. "

Steven D. Buckingham, Sequence Analysis Software Update, The Scientist, December 20, 2004

" Sequencher 4.10.1 contains a new feature that keeps track of protein and cDNA numbering in DNA assemblies. This ability greatly simplifies the task of comparing your experimental data to a genomic DNA reference when looking for mutations or other changes. This feature alone reinforces Sequencher as one of the premier tools for sequence analysis. "

David Adams, M.D Ph.D Clinical Investigator and Sequencher 4.10.1 beta tester

"I have been involved in DNA sequencing projects since I got my masters degree in bioinformatics in 2002. The programs I used for sequences analysis included Vector NTI from Invitrogen, PhredPhrap, Lasergene from DNAStar, and Sequencher. Sequencher is my favorite program not only because of its powerful SNP analysis functions but also because it is very easy to use and user friendly. I would like to recommend Sequencher to people who are doing SNP research projects and/or responsible for training students and colleagues who are going to do genotyping work. "

Zongying Xi, MD/MS, Department of Pharmaceutical Sciences St Jude Children's Research Hospital

"Thank you for sending the demo version of Sequencher. This seems to be wonderful software for phylogenetic and mutation studies. It clearly indicates start and stop codons in DNA sequences. Sequencher is easy to use and allowed us to quickly align sequences from various individuals. This software is very user friendly, and the instruction manual is very informative. The contig assembly tool is quite amazing in its speedy and time saving functions, which are the requirements for researchers in the biochemical field. I really got exited by running this software. "

Dr V.R.C. Murty, Department of Chemical Engineering Manipal Institute of Technology