Sanger Sequencing Software Support – Getting Started

The primary updates in Sequencing Analysis Software v7.0 are the following:
- Sequencing Analysis Software v7.0 supports installation on Microsoft Windows 7 (64-bit and 32-bit) and Microsoft Windows 10 Professional (64-bit) operating systems.
- Sequencing Analysis Software v7.0 uses KB Basecaller version 1.4.2.4 for basecalling.

Sequencing Analysis Software v7.0 supports data generated from the following instruments running all versions of Data Collection Software:

- Applied Biosystems SeqStudio Genetic Analyzer
- Applied Biosystems 3500 Genetic Analyzer
- Applied Biosystems 3500xL Genetic Analyzer
- Applied Biosystems 3130 Genetic Analyzer
- Applied Biosystems 3130xl Genetic Analyzer
- Applied Biosystems 3730 DNA Analyzer
- Applied Biosystems 3730xl DNA Analyzer
- Applied Biosystems 310 Genetic Analyzer

Sequencing Analysis Software v7.0 can be installed on capillary electrophoresis instrument computers with the following Data Collection Software versions:
- 3130/3130xl Data Collection Software v4.0
- 3730/3730xl Data Collection Software v4.0

This software has been extensively tested on Windows® 7 SP1 (32-bit version). While there are some indications that the software will run normally on the 64-bit version of Windows® 7 SP1 operating system, the 64-bit configuration is not officially supported. It is strongly recommended that this software be run on Windows® 7 SP1 (32-bit).

If installing on the instrument computer, the update will require a new computer and upgrading the Data Collection Software as well. Please click here for the Sequencing Analysis Software 6 datasheet.

The computer requirements are as follows:

• Minimum: 2 GHz CPU or faster
• 2 GB RAM
• 1 GB hard disk space for application

Recommended CPU: Core 2 Duo E8400/3.0 GHz

• 4 GB RAM
• 1 GB hard disk space

For the operating system, Sequencing Analysis Software 6 requires Windows® 7 Professional, 32-bit edition, service pack 1. Please click here for the Sequencing Analysis Software 6 datasheet.

The Sequencing Analysis Software 6 is compatible with the following data files:

• 310 PC, Data Collection Software v.3.0, 3.1
  
• 3100 series, Data Collection Software v.1.0, 1.1, 2.0
  
• 3130 series, Data Collection Software v.3.0, 3.1, 4
  
• 3730 series, Data Collection Software v.3.0, 3.1, 4
  
• 3500 series, Data Collection Software v.1.0, 1.1, 2

For more information, please click here for the Sequencing Analysis Software 6 datasheet.

The computer requirements are as follows:

• Minimum: 2.8 GHz Pentium® IV CPU or faster
• 1 GB RAM
• 40 GB hard disk space for application

Recommended CPU: Core 2 Duo E8400/3.0 GHz

• 2 GB RAM
• 320 GB hard disk space
• For the operating system, Sequencing Analysis Software v.5.4 requires either Windows® XP Professional, service pack 2 or 3, or Windows Vista™ (32-bit Business Edition), service pack 1. Please click here for the Sequencing Analysis Software v.5.4 datasheet.

Sequencing Analysis Software v.5.4 is compatible with the following data files:
310 PC, Data Collection Software v.3.0, 3.1
3100 series, Data Collection Software v.1.0, 1.1, 2.0
3130 series, Data Collection Software v.3.0, 3.1, 4
3730 series, Data Collection Software v.3.0, 3.1, 4
3500 series, Data Collection Software v.1.0, v1.1, 2
For more information, please click here for the Sequencing Analysis Software v.5.4 datasheet.

Unfortunately, Sequencing Analysis Software v.5.3.1 is not Windows® 7 compatible. Please click here for the Sequencing Analysis Software v.5.3.1 datasheet.

The computer requirements are as follows:

• Minimum: 733 MHz Pentium® IV CPU or faster
• 512 MB RAM
• 5 GB hard disk space for application

For the operating system, Sequencing Analysis Software v.5.3.1 requires Windows® 2000, service pack 3 or 4, Windows® XP Professional, service pack 2 or 3, or Windows® Vista (32-bit Business Edition). Please click here for the Sequencing Analysis Software v.5.3.1 datasheet.

The Sequencing Analysis Software v.5.3.1 is compatible with the following data files:
310 PC, Data Collection Software v.3.0
3100 series, Data CollectionSoftware v,1.0, 1.1, 2.0
3130 series, Data CollectionSoftware v.3.0
3730 series, Data Collection Software v.3.0

For more information, please click here for the Sequencing Analysis Software v.5.3.1 datasheet.

The primary updates in SeqScape Software v4.0 are the following:
- SeqScape Software v4.0 supports installation on Microsoft Windows 7 (64-bit and 32-bit) and Microsoft Windows 10 Professional (64-bit) operating systems.
- SeqScape Software v4.0 uses KB Basecaller version 1.4.2.4 for basecalling.

SeqScape Software v4.0 fully supports data generated from the following instruments running all versions of Data Collection Software:

- Applied Biosystems SeqStudio Genetic Analyzer
- Applied Biosystems 3500 Genetic Analyzer
- Applied Biosystems 3500xL Genetic Analyzer
- Applied Biosystems 3130 Genetic Analyzer
> - Applied Biosystems 3130xl Genetic Analyzer
- Applied Biosystems 3730 DNA Analyzer
- Applied Biosystems 3730xl DNA Analyzer
- Applied Biosystems 310 Genetic Analyzer (Note: Basecalling needs to be turned off to analyze 310 Genetic Analyzer data).

SeqScape Software v4.0 can be installed on capillary electrophoresis instrument computers with the following Data Collection Software versions:
- 3130/3130xl Data Collection Software v4.0
- 3730/3730xl Data Collection Software v4.0

If you received the error message about insufficient user privileges to start low level driver, you are most likely not logged in locally as the Administrator. Reboot the computer, change the domain to the local computer and log in as the Administrator.

Right click on “Computer” and select “Properties”. In the System section, look at the System Type and see if you have Windows® 7 Professional, 32-bit or 64-bit edition. Please write this down, as you will need this information during the install process.
To install the necessary driver:

1. Open a browser and go to https://www.ilok.com/#!home.
   
2. On the right-hand side of the page, you should see the “Free Download License Support” links.
   
   If your computer has the Windows® 7 Professional, 32-bit edition operating system, select the middle option (“Windows 32-bit XP, Vista, 7, 8”). If your computer has the Windows® 7 Professional, 64-bit edition operating system, choose the third option (“Windows 64-bit XP, Vista, 7, 8”).
   
   
   
   Note: If your browser gives you the choice to Run or Save, save the file. For the Internet Explorer® browser, you can choose the location to save the file. For Mozilla Firefox® and Google Chrome® browsers, the default location to save the file is the “Downloads” folder.
   
   
3. Run the installer. When the installation is complete, reboot the computer.

Right click on “Computer” and select “Properties”. In the System section, look at the System Type and see if you have Windows® 7 Professional, 32-bit or 64-bit edition. Please write this down, as you will need this information during the install process.
To install the necessary driver:

1. Open a browser and go to https://www.ilok.com/#!home.
2. On the right-hand side of the page, you should see the “Free Download License Support” links.
   
   If your computer has the Windows® 7 Professional, 32-bit edition operating system, select the middle option Windows 32-bit XP, Vista, 7, 8”). If your computer has the Windows® 7 Professional, 64-bit edition operating system, choose the third option (“Windows 64-bit XP, Vista, 7, 8”).
   
   
   
   Note: If your browser gives you the choice to Run or Save, Save the file. For the Internet Explorer® browser, you can choose the location to save the file. For Mozilla Firefox® and Google Chrome® browsers, the default location to save the file is the “Downloads” folder.
   
   
3. Run the installer. When the installation is complete, reboot the computer.

This software has been extensively tested on Windows® 7 SP1 (32-bit version). While there are some indications that software will run normally on the 64-bit version of Windows® 7 SP1 operating system, the 64-bit configuration is not officially supported. It is strongly recommended that this software is run on Windows® 7 SP1 (32-bit).

If installing on the instrument computer, the update will require a new computer and upgrading the Data Collection Software as well. Please click here for the SeqScape® Software v.3 datasheet.

The computer requirements are as follows:

• Minimum: 2.0 GHz or faster Intel® processor
• 2 GB RAM
• 1 GB hard disk space for application

Recommended CPU: Core 2 Duo E8400/3.0 GHz

• 4 GB RAM
• 1 GB hard disk space

For the operating system, SeqScape® Software v.3 requires Windows 7 Professional, 32-bit edition, service pack 1. Please click here for the SeqScape® Software v.3 datasheet.

The SeqScape® Software v.3 is compatible with the following data files:

• 310 PC, Data Collection Software v.3.0, 3.1
  
• 3100 series, Data Collection Software v.1.0, 1.1, 2.0
  
• 3130 series, Data CollectionSoftware v.3.0, 3.1, 4
  
• 3730 series, Data Collection Software v.3.0, 3.1, 4
  
• 3500 series, Data Collection Software v.1.0, 1.1, 2
  
• 3500 Dx series, Data Collection Software v.1.0

For more information, please click here for the SeqScape® Software v.3 datasheet.

This software is not Windows® 7 compatible. Please click here for the SeqScape® Software v.2.7 datasheet.

The computer requirements are as follows:

• Minimum: 2.8 GHz Pentium® IV CPU or faster
• 1 GB RAM
• 40 GB hard disk space for application
•  

Recommended CPU: Core 2 Duo E8400/3.0 GHz

• 2 GB RAM
• 320 GB hard disk space

For the operating system, SeqScape® Software v.2.7 requires either Windows® XP Professional, service pack 2 or 3 or Windows Vista™ (32-bit Business Edition), service pack 1. Please click here for the SeqScape® Software v.2.7 datasheet.

The SeqScape® Software v.2.7 is compatible with the following data files:

• 310 PC, Data Collection Software v.3.0, 3.1
  
• 3100 series, Data Collection Software v.1.0, 1.1, 2.0
  
• 3130 series, Data Collection Software v.3.0, 3.1, 4
  
• 3730 series, Data Collection Software v.3.0, 3.1, 4
  
• 3500 series, Data Collection Software v.1.0, 1.1, 2

Please note, upgrade will require Data Collection Software v.3.1 on the 3130 and 3730 series instruments for co-installation. System upgrade may be required.

For more information, please click here for the SeqScape® Software v.2.7 datasheet.

The primary updates in Variant Reporter Software v3.0 are the following:
- Variant Reporter Software v3.0 supports installation on Microsoft Windows 7 (64-bit and 32-bit) and Microsoft Windows 10 Professional (64-bit) operating systems.
- Variant Reporter Software v3.0 uses KB Basecaller version 1.4.2.4 for basecalling.

Variant Reporter Software v3.0 fully supports data generated from the following instruments running all versions of Data Collection Software:

- Applied Biosystems SeqStudio Genetic Analyzer
- Applied Biosystems 3500 Genetic Analyzer
- Applied Biosystems 3500xL Genetic Analyzer
- Applied Biosystems 3130 Genetic Analyzer
- Applied Biosystems 3130xl Genetic Analyzer
- Applied Biosystems 3730 DNA Analyzer
- Applied Biosystems 3730xl DNA Analyzer

This software has been extensively tested on Windows® 7 SP1 (32-bit version). While there are some indications that the software will run normally on the 64-bit version of Windows® 7 SP1 operating system, the 64-bit configuration is not officially supported. It is strongly recommended that this software is run on Windows® 7 SP1 (32-bit).

If installing on the instrument computer, the update will require a new computer and upgrading the Data Collection Software as well. Please click here for the Variant Reporter® Software v.2 datasheet.

The computer requirements are as follows:

• Minimum: 2.0 GHz or faster Intel® processor
• 2 GB RAM
• 1 GB hard disk space for application

Recommended CPU: Core 2 Duo E8400/3.0 GHz

• 4 GB RAM
• 1 GB hard disk space

For the operating system, Variant Reporter® Software v.2 requires Windows® 7 Professional, 32-bit edition, service pack 1. Please click here for the Variant Reporter® Software v.2 datasheet.

The Variant Reporter® Software v.2 is compatible with the following data files:

• 3130 series Data Collection Software 4
• 3730 series Data Collection Software 4
• 3500 series Data Collection Software 20

For more information, please click here for the Variant Reporter® Software v.2 datasheet.

Unfortunately, Variant Reporter® Software v.1.1 is not Windows® 7 compatible.
Please click here for the Variant Reporter® Software v.1.1 datasheet.

The computer requirements are as follows:

• Minimum: 2.8 GHz Pentium® IV CPU or faster
• 512 MB RAM
• 40 GB hard disk space for application

Recommended CPU: Core 2 Duo E8400/3.0 GHz

• 1 GB RAM
• 320 GB hard disk space

For the operating system, Variant Reporter® Software v.1.1 requires either Windows® XP Professional, service pack 3, or Windows Vista™ (32-bit Business Edition), service pack 1. Please click here for the Variant Reporter® Software v.1.1 datasheet.

The Variant Reporter® Software v.1.1 is compatible with the following data files:

• 310 PC, Data Collection Software v.3.1
  
• 3130 series Data Collection Software v.3.1
  
• 3730 series Data Collection Software v.3.1
  
• 3500 series Data Collection Software v.1.0

Please note, ABI PRISM® 310 data will have to be pre-analyzed in Sequencing Analysis Software before importing into Variant Reporter®. For more information, please click here for the Variant Reporter® Software v.1.1 datasheet.

This library is an add-on to MicroSEQ ID 16S rDNA 500 Library v2013 (Cat. No. 4398220).

We recommend using MicroSeq ID 16S rDNA 500 Supplemental Library only when the MicroSEQ ID 16S rdna 500 Library v2013 database generates a match <99% but has met all other acceptance criteria.

There are 7,138 entries of bacterial species.

The library entry format for MicroSeq ID 16S rDNA 500 Supplemental Library contains strain information in the Comments column. In addition, the Source column has NCBI information for all entries and the Entry Number column includes accession number for the sequences.

The special character ^ indicates that the sequence was derived from the type strain.

• The software is compatible with 3500 Data Collection v3.1 software which allows 14-day on-instrument usage time for reagents.
• Improved reporting format: More information is presented on fewer pages for better printed reports.
• New "Lifetechsupport" user group has been added to assist in the service and support of the MicroSEQ Microbial ID System by a Thermo Fisher Scientific representative.
• Windows 7, 64-bit compatibility: The Lite edition of MicroSEQ ID Software is compatible with both 32- and 64-bit Windows 7 operating systems. The Full edition is compatible only with 32-bit Windows 7 operating system.

Data from the following instruments are compatible with MicroSEQ ID Microbial Identification Software v3.1:

310, 3100-Avant, 3100, 3130/3130xl, 3500/3500xL, and 3730/3730xl

MicroSEQ ID Microbial Identification Software v3.1 is only compatible with 3500 Data Collection software version 3.1.

MicroSEQ ID Microbial Identification Software v3.0 is only compatible with 3500 Data Collection software version 1.1.

The Full version supports 3500 Genetic Analyzer instrument control. The Lite version supports offline analysis only.

Additional copies of existing libraries are not needed when upgrading to MicroSEQ ID Microbial Identification Software version 3.1.

MicroSEQ ID Microbial Identification Software Lite v3.1 Bundle, Cat. No. A38912, includes all the components of Cat. No. A30374 and in addition, it includes the validated 500 16S rDNA supplemental bacterial library. Please note that Cat. No. A38912 will be replacing Cat. No. A30374.

The components of the MicroSEQ ID Microbial Identification Software Lite v3.1 Bundle (Cat. No. A38912) are the following:

• MicroSEQ ID software version 3.1 (Lite)
• 500 16S rDNA bacterial library
• 500 16S rDNA supplemental bacterial library
• 16S Full Gene bacterial library
• Fungal library

MicroSEQ ID Microbial Identification Software v3.1 Bundle, Cat. No. A38447, includes all the components of Cat. No. A30371 and in addition, it includes the validated 500 16S rDNA supplemental bacterial library. Please note that Cat. No. A38447 will be replacing Cat. No. A30371.

The components of the MicroSEQ ID Microbial Identification Software v3.1 Bundle (Cat. No. A38447) are the following:

• MicroSEQ ID software version 3.1 (Full)
• 500 16S rDNA bacterial library
• 500 16S rDNA supplemental bacterial library
• 16S Full Gene bacterial library
• Fungal library

The MicroSEQ ID Microbial Identification Software, Lite, version 3.1.3 allows you to easily identify and classify bacterial or fungal sequences by comparing them to a validated microbial library (available separately). This Lite version of the software is for use on a stand-alone PC (not connected to the genetic analyzer) for data analyses only.

No new features were introduced into MicroSEQ ID Microbial Identification Software, Lite, version 3.1.3, compared to version 3.1. MicroSEQ ID Microbial Identification Software, Lite, version 3.1.3 is a stand-alone version of MicroSEQ ID Microbial Identification Software, version 3.1.3.

The Lite and System edition of MicroSEQ ID Microbial Identification Software are now compatible with 64-bit Windows 10 operating systems.

Here are the recommended computer specifications for the MicroSEQ ID Microbial Identification Software, Lite, version 3.1.3:

- Processor: Intel Core i5 processor, 2.8 GHz or faster
- Hard drive: ≥250 GB for software installation and data storage
- Memory: ≥16 GB
- Operating System (OS): Windows 10 IOT, 64‑bit

IMPORTANT! We strongly recommend that you use computers that are provided by Thermo Fisher Scientific. All validation and verification studies were performed using Thermo Fisher Scientific computers.

MicroSEQ ID Microbial Identification Software, Lite, version 3.1.3 is supported on Microsoft Windows 10, 64-bit operating system.

MicroSEQ ID 16S rDNA Full Gene Library v2.0 is the same as MicroSEQ ID 16S rDNA Full Gene Library 1.0 but in USB format. No new content has been added.

The only difference is that Cat. No. A46365 is available in USB format, otherwise the content is the same between the two catalog numbers.

The components of the MicroSEQ ID Microbial Identification Software Lite v3.1.3 and Libraries Bundle (Cat. No. A46530) are the following:
- MicroSEQ ID Microbial Identification Software, version 3.1.3
- MicroSEQ ID Microbial Identification Software, version 3.1.3 License
- MicroSEQ ID Fungal Gene Library, v2018
- MicroSEQ ID 16S rDNA 500 Microbial Library, v2019
- MicroSEQ ID 16S rDNA Full Gene Library

The MicroSEQ ID Microbial Identification Software v3.1.3, with All Software Libraries Kit (Cat. No. A48593) includes the following components:
MicroSEQ ID Microbial Identification Software v3.1.3
MicroSEQ ID Microbial Identification Software v3.1.3 License
MicroSEQ ID Supplemental Library v2019
MicroSEQ ID Supplemental Library v2019 License
MicroSEQ ID 16S rDNA 500 Microbial Library, v2019
MicroSEQ ID 16S rDNA 500 Microbial Library, v2019 License
MicroSEQ ID Fungal Gene Library, v2018
MicroSEQ ID Fungal Gene Library, v2018 License
MicroSEQ ID v2.0 Full Gene Library

The MicroSEQ ID Microbial Identification Software v3.1.3, Lite, with All Software Libraries Kit (Cat. No. A48594) includes the following components:
MicroSEQ ID Microbial Identification Software, v3.1.3, Lite, WIN 10
MicroSEQ ID Microbial Identification Software, v3.1.3, Lite License
MicroSEQ ID Supplemental Library v2019
MicroSEQ ID Supplemental Library v2019 License
MicroSEQ ID 16S rDNA 500 Microbial Library, v2019
MicroSEQ ID 16S rDNA 500 Microbial Library, v2019 License
MicroSEQ ID Fungal Gene Library, v2018
MicroSEQ ID Fungal Gene Library, v2018 License
MicroSEQ ID v2.0 Full Gene Library

The minimum system requirements for MicroSEQ ID Microbial Identification Software v3.1.3 are the following:
- Intel Core i7 Processor, 3.1 GHz or faster
- Microsoft Windows 10 OS, Service Pack 1, 64-bit
- At least 16 GB of RAM
- At least 250 GB of disk space for software

The computer that is compatible with MicroSEQ ID Software v3.1.3 (system installation) is the Dell Optiplex XE2 with Win10 IOT 2016-64-bit.

The computers that are compatible with MicroSEQ ID Software v3.1.3 (Lite installation) are the Dell Optiplex XE2 with Win10 IOT 2016-64-bit, Dell Latitude E5570 Laptop with Win10 IOT 2016-64-bit, and Dell Latitude E5580 Laptop with Win10 IOT 2016-64-bit.

Yes, please see here.

Minor Variant Finder Software allows you to identify somatic mutations confidently down to 5% with 95% sensitivity and 99% specificity.

Minor Variant Finder Software subtracts sequencing background noise to allow for detection of rare minor variants.

Forward and reverse sequences for the sample, as well as forward and reverse sequences for a control sample with the same primary sequence are needed to analyze a sample in Minor Variant Finder Software.

Yes, the software allows reviewing of the original sequences of the test and control samples, as well as the noise-reduced sequence, all on the same page.

Variants can be exported in .vcf and .csv file formats.

Yes, Minor Variant Finder Software can be used to verify NGS data.