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Applied Biosystems™ InnoviGene™ Suite Software

Catalog No. A40001765
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Catalog No. A40001765 Supplier Applied Biosystems™ Supplier No. A40001765

Please call Customer Service at 1-800-234-7437 or send an email to help@thermofisher.com for assistance.

Description

InnoviGene Suite software enables you to analyze and manage capillary electrophoresis sequencing & fragment analysis data generated by Applied Biosystems genetic analyzers.

Applied Biosystems InnoviGene Suite software enables you to analyze and manage capillary electrophoresis sequencing and fragment analysis data generated by Applied Biosystems genetic analyzers. The software provides a streamlined workflow to guide you through uploading and analyzing the data and generating reports.

InnoviGene Suite includes SAE administrator console software with security, audit, and electronic signature (SAE) functions that support compliance with guidelines on electronic records security and prevents unauthorized access to the instrument.

The software is delivered via a download link sent to you after purchase.

Applications within InnoviGene Suite

InnoviGene Suite allows you to create projects for use with other applications that are integrated into the software. These applications enable you to complete an end-to-end workflow using projects that contain related files. The applications available depend on the type of InnoviGene Suite purchased ('sequencing' or 'fragment analysis').

Sequence Quality Check application (Innovigene Suite for sequencing)—enables you to perform the following activities:

  • View the quality information for trace files
  • Change quality settings and reanalyze trace files
  • Perform comparative analysis across multiple trace files

Sequence Identity application (InnoviGene Suite for sequencing)—enables you to view the assembly of multiple files compared to a reference and view basecall mismatches. Specifically, you can perform the following activities with the application:

  • Basecalling, quality value assignment, and mixed base identification
  • Trimming low-quality ends from each sequence, if the setting is active
  • Identifying poor-quality samples
  • Assembling the samples against the reference sequence and generating a specimen consensus sequence
  • Reviewing the basecalling quality values and consensus quality values
  • Identifying mismatches by aligning and comparing specimen sequences to the reference sequence. A mismatch is a position in the specimen that does not match with the reference sequence. Mismatches include base changes, insertions, and deletions.
  • Assigning specimen status based on alignment with the reference sequence and coverage criteria
  • Editing basecalls in samples or the consensus
  • Generating reports and results for export in CSV format

STR Typing application (InnoviGene Suite for fragment analysis)—the STR Typing application is genotyping software that uses short tandem repeat (STR) data. It enables you to perform the following activities:

  • Analyze a mixture of DNA fragments, separated by size
  • Provide a profile of the separation
  • Calculate the sizes of the fragments
  • Determine the alleles present in fragment analysis sample (FSA) files

Specifications

Product Line InnoviGene
Format Software
For Use With (Application) Sanger Sequencing
For Use With (Equipment) Applied Biosystems™ Genetic Analyzers
License 3 Years
Product Type Sequencing Software
Quantity 5 Users
Sequencing Type Sanger Sequencing

Frequently Asked Questions (FAQs)

Can our existing SeqScape project templates or ROIs be used or adapted for the InnoviGene Suite?

SeqScape templates and RDGs cannot be imported into the InnoviGene Suite. If you have a GenBank file (.gb file) with non-overlapping ROIs, it can be imported into the InnoviGene Suite. Please note that some features in .gb files may be ignored by the InnoviGene Suite. For detailed information on .gb file compatibility, please refer to the relevant sections in the Getting Started Guide (GSG) or User Guide (UG) that can be found here: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN1000299-InnoviGeneSuiteSoftware-EFI.pdf and Capillary Electrophoresis Software Support Center.
Where is the data stored in InnoviGene Suite, and will it be accessible to other members of our group later?

The InnoviGene Suite data is stored on your local computer in a folder location specified by the user during the installation of InnoviGene Suite software. If another member of your group is added to the same SAE Administrator Console, the InnoviGene Suite allows you to share items with those same users within the InnvoiGene Suite. If they are using a different SAE Administrator Console License, trace files, projects, and other files can be exported and later imported into another InnoviGene Suite instance and Capillary Electrophoresis Software Support Center.

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Since the InnoviGene Suite is browser-based, can you confirm that our data is not being transmitted outside our computer systems (e.g., back to ThermoFisher Connect)?

The InnoviGene Suite does not have direct access to ThermoFisher Connect. With browser-based access, only colleagues on the same network and with user credentials on the same instance of the InnoviGene Suite may have access to the data. During installation of InnoviGene Suite software, the user will specify a folder location where all project data will be stored. Users will have to export files from the InnoviGene Suite and send to Thermo Fisher Scientific personnel, for troubleshooting purposes or data review. and Capillary Electrophoresis Software Support Center.
Can InnoviGene Suite software be co-installed with Applied Biosystems legacy software?  

Co-installation with InnoviGene Suite software was tested for the following software:
- GeneMapper v6.1​
- Sequencing Analysis v8.0 (without the SDB license)
- SeqScape v4.1​
- Variant Reporter v3.1​
- Plate Manager v2.1.0

   Note: There is a known FlexNet licensing conflict between InnoviGene Suite and the SeqA 8 + SDB license and these softwares should not be co-installed. and Capillary Electrophoresis Software Support Center.
What antivirus software is the InnoviGene Suite compatible with? 

The InnoviGene Suite is compatible with the following various antivirus software:
- Symantec™ Endpoint Protection
- McAfee®Endpoint Security
- Norton Internet Security™
- Microsoft® Defender antivirus software and Capillary Electrophoresis Software Support Center.
In InnoviGene Suite software, which formats can reference files be in?

In InnoviGene Suite software, reference files can be in GB (GenBank) or FASTA format. and Capillary Electrophoresis Software Support Center.
Where can I find a list of software error messages for InnoviGene Suite software? 

A comprehensive list of software error messages for InnoviGene Suite software can be found in the user guide (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN1000299-InnoviGeneSuiteSoftware-EFI.pdf). Specifically, the Troubleshooting Appendix within the user guide provides detailed information about common error messages and their possible causes. and Capillary Electrophoresis Software Support Center.
How do I back up InnoviGene Suite software data?

In InnoviGene Suite software, you have the option to individually export custom items as needed for backup purposes. Additionally, you can follow the instructions provided in the user guide (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN1000299-InnoviGeneSuiteSoftware-EFI.pdf) to back up the entire contents of the software.

You can specify a folder where the backup contents will be stored. If needed, this folder can be used to restore the software and data, bringing it back to the state it was in at the time of the backup. and Capillary Electrophoresis Software Support Center.
Where can I access training material for InnoviGene Suite software? 

An introductory e-learning course for InnoviGene Suite software is available on EducationConnect. Instructions for accessing the e-learning course can be found here: https://www.brainshark.com/1/player/thermofisher?fb=0&r3f1=&custom=innovigene_course_instructions. Contact thermofisher.com/support for additional information on training options. and Capillary Electrophoresis Software Support Center.
Can I directly access Thermo Fisher Connect through the InnoviGene Suite?

The InnoviGene Suite does not have direct access to Thermo Fisher Connect. The InnoviGene Suite is installed on a local computer and has browser-based access. Data can be imported into InnoviGene Suite software projects from the Data Manager, local computer, or network drive. With browser-based access, you can access the software from any computer on the same network and share data with colleagues using the same instance of the InnoviGene Suite. and Capillary Electrophoresis Software Support Center.
In the InnoviGene Suite, I am getting an SAE authentication error during installation. What should I do?

If you encounter an SAE authentication error during the installation of the InnoviGene Suite, please follow these steps:
- Review the Getting Started Guide: Refer to the InnoviGene Suite's Getting Started Guide and ensure that you have followed the recommended configuration steps. Pay particular attention to the section related to opening the appropriate ports to allow communication between the software and the SAE Administrator console.
- Check connectivity: Verify that there is proper connectivity between the computer running the InnoviGene Suite application and the SAE Administrator console computer.
- Verify time synchronization: Make sure that the time difference between the InnoviGene Suite application and the separate computer running the SAE Administrator Console is less than 5 min. Time synchronization is crucial for establishing a secure and authenticated connection. and Capillary Electrophoresis Software Support Center.
I forgot my password for the InnoviGene Suite, how can I reset it? 

If you have forgotten your password for the InnoviGene Suite, the recommended course of action is to contact your SAE (System Administrator Equivalent) Administrator. The SAE Administrator has the necessary permissions and access to reset user passwords within the software. However, if the SAE Administrator account password itself is forgotten, the software will need to be re-installed. and Capillary Electrophoresis Software Support Center.
In the InnoviGene Suite, what can impact the analysis speed?

The analysis speed in the InnoviGene Suite can be influenced by several factors. These include:
- Computer environment: The specifications of your computer, such as processor speed, memory, and storage capacity, can impact the analysis speed. Additionally, if there are other resource-intensive programs running simultaneously, they may affect the software's performance. Network conditions can also play a role, especially when remotely accessing the software.
- Within the software: The number of files in the database can impact the analysis speed. If there is a large volume of files, it may take longer to process and analyze the data. Concurrent users working with a significant number of files can also affect the performance.
- Within the project: The number of specimens and the number of sample files within each specimen can impact the analysis speed. Additionally, the size of the reference sequence(s) used in the project can also influence the processing time. and Capillary Electrophoresis Software Support Center.
Is there a sample number limitation in the InnoviGene Suite?

The performance of the InnoviGene Suite can be impacted by various factors, such as computer specifications and project complexity. While there is no specific sample number limitation mentioned, the performance of the software may be influenced by the number of specimens, the number of samples per specimen, and the length of the reference sequence.

As the number of specimens and samples increases, along with longer reference sequences, the software may require more computational resources and processing time. It is essential to consider the capabilities of your computer, including its processing power, memory, and storage capacity, to enable optimal performance when working with a large number of samples. and Capillary Electrophoresis Software Support Center.
In the InnoviGene Suite, is there a limit to file size or reference length?

Yes, in the InnoviGene Suite, there are limits to the file size and reference length. The maximum file size for a reference is 25 MB, and the maximum reference length is 100 kb. and Capillary Electrophoresis Software Support Center.
In the InnoviGene Suite, I am not able to view my trace in the data viewer. What should I do?

If you are unable to view your trace in the data viewer of the InnoviGene Suite, please follow these steps:
- Make sure that a trace is selected.
- Expand the sample details view: If the trace is not visible or appears to be cut off, try expanding the sample details view. You can do this by dragging the divider up or down to expand the sample details view and make the trace visible. and Capillary Electrophoresis Software Support Center.
In the InnoviGene Suite, where can I find a list of mismatches in my Sequence Identity project? 

In the InnoviGene Suite, you can find a list of mismatches in your Sequence Identity project in the following locations: Results summary mismatches details, mismatches table in the Alignment tab, the exported mismatches.csv, and in the pdf report if mismatch summary is included. and Capillary Electrophoresis Software Support Center.
What does the red circle over my trace in the InnoviGene Suite indicate?

In the InnoviGene Suite, a red circle over your trace indicates a discrepancy between the trace and the consensus sequence. Reviewing these regions can help in identifying and investigating any variations or discrepancies that may require further analysis or confirmation. and Capillary Electrophoresis Software Support Center.
In the InnoviGene Suite, what basecall settings are recommended for the Sequence Identity application?

For the Sequence Identity application in the InnoviGene Suite, we recommend using the following basecalling options, Mixed basecalling and PCR stop, with either KB or Smart Deep Basecaller (SDB) with Classic View. Traces basecalled with SDB Enhanced View analysis protocol should not be used in the Sequence Identity Application as Enhanced View removes secondary peaks. and Capillary Electrophoresis Software Support Center.
Can I set quality flags settings for all projects in the InnoviGene Suite?

In the InnoviGene Suite, you can set quality flags in a project template for the Sequence Identity application. In the process of creating a project template, you will reach a step titled ''Quality flags''. Here you can enter the information for the quality flags settings. and Capillary Electrophoresis Software Support Center.
Can I re-basecall samples in the InnoviGene Suite?

You can re-basecall trace files in the InnoviGene Suite. This functionality is available in both the Sequence Identity application and the Sequence Quality Check application. and Capillary Electrophoresis Software Support Center.
How can I access the InnoviGene Suite from another computer?

Here are instructions to access the InnoviGene Suite from another computer:
- Open a web browser
- Enter https://<<[IP address of the computer where InnoviGene Suite software is installed]:8081/platform-web/dataviewer (eg., https://<<11.111.11.1:8081/platform-web/dataviewer)
- Press the Enter key
- Sign in with User Credentials and Capillary Electrophoresis Software Support Center.
How do I obtain the software license for the InnoviGene Suite? 

After purchasing the InnoviGene Suite, you should receive an email containing the software license details and instructions for activating the license. It is important to check your email inbox, including any spam or junk folders, to ensure that you do not miss this email. and Capillary Electrophoresis Software Support Center.
Do I need internet access to install/run the InnoviGene Suite?

You do not need internet access to install or run the InnoviGene Suite. If the computer where you plan to install the software does not have internet access, you can download the installer and license file from another computer with internet access and transfer them to the computer running the software. Once the software is installed, it can be used without an internet connection. However, please note that certain features or functionalities within the software may require internet access, such as accessing online resources or downloading updates. and Capillary Electrophoresis Software Support Center.
How often should I archive and backup data in the InnoviGene Suite?

When archiving and backing up data in the InnoviGene Suite, factors to consider include the volume of data generated, the criticality of the data, and the potential risks associated with data loss or system failures. To support the integrity and availability of your data, it is generally advisable to establish a regular backup schedule depending on the volume of data.

The frequency of archiving and backing up data in the InnoviGene Suite will vary depending on factors such as your organizational policy, throughput, and computer specifications. We recommend following your organization's data management policies and guidelines when determining the frequency of archiving and backing up data. and Capillary Electrophoresis Software Support Center.
In the Data viewer section, how many samples can be viewed at a time in the InnoviGene Suite?

1 to 4 sample details can be viewed simultaneously in the InnoviGene Suite. However, the card view option can be chosen for a quick overview of all traces in the project. and Capillary Electrophoresis Software Support Center.
What file types can be exported in the InnoviGene Suite?

From ''export samples'', you can export files in the following formats: annotation,txt, phd.1, ab1, peaks.csv, traces.csv, image files (pdf, jpeg, png), FASTA, seq, qual, and QC report.

From ''export results'' in SeqID, you can export trim and filter settings csv, alignment and assembly settings csv, assembly results csv, alignment results csv, mismatch csv, FASTA files of reference and consensus, and PDF reports of QC and summary. and Capillary Electrophoresis Software Support Center.
How can I share my InnoviGene Suite data with other colleagues?

Users within the same instance of the InnoviGene Suite can share custom items such as data, projects, templates, reports, and more by using the ''share'' function. To access this feature in SeqID, simply navigate to the ''more action'' menu in the sections of interest. In addition, the software supports connection to a network drive for import of data and export of reports and results. and Capillary Electrophoresis Software Support Center.
Can I use the InnoviGene Suite license on multiple computers?

The InnoviGene Suite license is intended for a single installation instance. This means that the license is tied to a specific computer where the software is installed. However, with browser-based access, you can access the software from any computer on the same network. It is important to note that each license allows up to five concurrent users. and Capillary Electrophoresis Software Support Center.
Will I get a reminder for expiration of the InnoviGene Suite license?

Yes, a reminder for expiration of the InnoviGene Suite license will be sent 15 days in advance of the expiration date. Additionally, you can also view the license expiry date at any time by navigating to the ''System'' section, then selecting ''Applications and License'', and selecting the ''Licenses'' tab. This allows you to stay informed about your license status and take appropriate actions for renewal or any necessary updates. and Capillary Electrophoresis Software Support Center.
Can the InnoviGene Suite be installed on capillary electrophoresis instrument computers? 

No, the InnoviGene Suite should not be co-installed with the Data Collection Software on capillary electrophoresis instrument computers. The InnoviGene Suite is designed to be installed on separate computers to ensure optimal performance and functionality. and Capillary Electrophoresis Software Support Center.
Does the InnoviGene Suite replace Variant Reporter and SeqScape software?

We continue to support Variant Reporter and SeqScape software as we work alongside on enhancing and expanding the capabilities of the InnoviGene Suite. and Capillary Electrophoresis Software Support Center.
What instrument files are compatible with the InnoviGene Suite?  

The InnoviGene Suite is compatible with the following instruments:
- SeqStudio Flex Series Genetic Analyzers
- SeqStudio Genetic Analyzer
- 3730/3730xl DNA Analyzers
- 3500/3500xL Genetic Analyzers and Capillary Electrophoresis Software Support Center.
What are the minimum computer specifications for the InnoviGene Suite?

For the InnoviGene Suite, the minimum computer requirements are:
Operating system - Windows 10 or 11 (64 bit) Processor; 1 GHz or faster with at least 4 cores
Memory - Recommended: 16 GB RAM; Minimum: 8 GB RAM
Hard drive free space - 100 GB
Monitor - Optimal: 1920 × 1080 resolution; Minimum: 1280 × 800 resolution and Capillary Electrophoresis Software Support Center.

For Research Use Only. Not for use in diagnostic procedures.