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Sanger Sequencing and Fragment Analysis Software
We offer a wide portfolio of Applied Biosystems software solutions for viewing and interpreting your Sanger sequencing and fragment analysis results. Learn about our free tools and commercially available products below.
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Visit our Capillary Electrophoresis Software Support Center.
Data collection software
| Software | Description | Operating system requirements |
|---|---|---|
Data Collection Software | Data Collection Software is an integrated software for instrument control, data collection, quality control, base-calling, and size-calling of samples. Operation of the instrument is dependent on this software. | |
SeqStudio Genetic Analyzer software Download the latest software update › | SeqStudio Genetic Analyzer software is the embedded software on the SeqStudio instrument. | Not Applicable |
| Platform for Science, Sanger Sequencing Solution | Supports end-to-end sample tracking from sample accessioning to sequencing including lineage, volumes and concentrations. Enables managers to look for bottlenecks in sample processing and lab scientists to identify samples ready for processing at each step in the process. | Platform for Science |
Sanger sequencing software
Viewer
| Software | Description | Operating system requirements |
|---|---|---|
| Sequence Scanner Software allows you to view, edit, print, and export data generated using Applied Biosystems genetic analyzer instruments after data has been processed by Sequencing Analysis Software. | Windows™ 7 |
| The Quality Check (QC) Module evaluates trace quality. The easy-to-interpret analysis summary gives a snapshot of Sanger sequence trace quality. The Trace Details page allows you to evaluate and edit traces as needed. The Flag Settings page allows you to adjust quality thresholds. | Free access on Thermo Fisher Cloud |
Sequence Scanner Software v2.0
Primary analysis tool
| Software | Description | Operating system requirements |
|---|---|---|
Sequencing Analysis Software uses a base-caller algorithm that performs base calling for pure and mixed base calls. The software analyzes, displays, edits, saves, and prints sample files that are generated from Applied Biosystems DNA analyzers and genetic analyzers. | Windows™ 7 | |
The Smart Deep Basecaller (SDB) is an innovative new basecalling algorithm that allows you to obtain improved Sanger sequencing output with reduced manual review time. The Smart Deep Basecaller is available for use in Sequencing Analysis Software 8. | Windows™ 10 |
Secondary analysis tool
| Software | Description | Operating system requirements |
|---|---|---|
Minor Variant Finder Software enables 5% somatic variant detection using Sanger sequencing. The improved sensitivity makes Sanger sequencing a fast, cost effective, and accurate way to call low-frequency somatic variants where the number of relevant targets is limited. | Windows™ 7 SP1, 32-bit or 64-bit or Windows™ 10 | |
| SeqScape Software is a resequencing package designed for mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification, and sequence confirmation. It provides library functions for comparison to a known group of sequences, as well as features to assist with 21 CFR Part 11 compliance (Security, Audit and electronic signature features), which can be important in clinical research labs. | Windows™ 7 | |
| Download trial version › | Variant Reporter Software is designed for reference-based and non-reference-based analysis such as mutation detection and analysis, SNP discovery and validation, and sequence confirmation. The robust algorithms will call SNPs, mutations, insertions, deletions, and heterozygous insertions⁄deletions for data generated using Applied Biosystems genetic analyzers. | Windows™ 7 |
| The Variant Analysis (VA) Module provides fast analysis of Sanger sequencing data. The VA Module can automatically retrieve reference sequences from the genomic database, report variants with genomic coordinates, and report genomic annotations for SNPs. With highly overlapped forward/reverse strands, the VA Module reports very high sensitivity for SNP calls. The VA Module also reports and exports variant files in standard .vcf format. There is no software maintenance required from users. | Free access on Thermo Fisher Cloud | |
| The Next-Generation Confirmation (NGC) Module lets users compare results from standard NGS variant files with results from Sanger sequencing instruments within the Thermo Fisher Cloud environment. Critical decisions often require validation of NGS results using robust Sanger sequencing. The NGC module provides fast analysis of AB1 files and reports variants in genomic coordinates. The results are automatically annotated with known SNPs from the current genomic database. | Free access on Thermo Fisher Cloud | |
| MicroSEQ ID Microbial Identification Software is a tool for identification of bacteria and fungi. The software analyzes data generated using an Applied Biosystems MicroSEQ chemistry kit and an Applied Biosystems capillary-based genetic analyzer. | Windows™ 7 | |
| MicrobeBridge Software is a streamlined, desktop software solution that connects DNA sequences generated on Applied Biosystems Sanger sequencers with the Centers for Disease Control and Prevention (CDC)’s MicrobeNet™ database for bacterial identification using 16S rRNA gene sequencing analysis. There is no need for local database setup, so computer resources are easily developed. | ||
| The Applied Biosystems SeqScreener Gene Edit Confirmation App (SGC) is a free and user-friendly software to determine the range and frequency of mutations generated in CRISPR-Cas9 experiments. |
Minor Variant Finder Software
Variant Reporter Software
Variant Analysis (VA) Module
Next Generation Confirmation (NGC) Module
MicroSEQ ID Microbial Identification Software
MicrobeBridge Software
SeqScreener Gene edit confirmation app (SGC)
Fragment analysis software
Sizing software
| Software | Description | Operating system requirements |
|---|---|---|
| Peak Scanner module is a DNA fragment sizing software that performs DNA fragment analysis, separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using Applied Biosystems genetic analyzers. | Free access on Thermo Fisher Cloud |
| Microsatellite Analysis Software(MSA) is a microsatellite genotyping software that allows you to analyze a mixture of DNA fragments, separated by size. This analysis provides a profile of the separation, precisely calculates the sizes of the fragments, and determines the microsatellite alleles present in the sample. Microsatellite Analysis is commonly used for Microsatellite Instability in cancer, Triplet Repeat Expansion in neurodegenerative diseases, Species Identification & Characterization; and Human Sample Authentication. | Free access on Thermo Fisher Cloud |
| Peak Scanner Software is a DNA sizing software that can either be downloaded for free or purchased for free as a software kit. | Windows™ 7 |
| GeneMapper Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. This software specializes in multi-application functionality, including Applied Biosystems amplified fragment length polymorphism (AFLP) analysis, loss of heterozygosity (LOH), microsatellite, and SNP genotyping analysis. In addition, the security and audit features help users meet 21 CFR 11 requirements. |
Peak Scanner Software
GeneMapper Software
Primer design tool
| Software | Description | Operating system requirements |
|---|---|---|
The free, online Primer Designer Tool allows you to search for the right PCR/Sanger sequencing primer pair from a database of ~650,000 predesigned primer pairs for resequencing the human exome and human mitochondrial genome. | Web tool | |
| Methyl Primer Express Software v1.0 enables you to design high-quality PCR primers for methylation mapping experiments. Simply cut and paste in your region of interest. The tool searches for CpG islands and simulates bisulfite modification of DNA in silico. |
Primer Designer Tool
For Research Use Only. Not for use in diagnostic procedures.