Data Analysis Software

After electrophoresis, data collection software creates a sample file of the raw data. Using downstream software applications, further data analysis is required to translate the collected color-data images into the corresponding nucleotide bases or fragment analysis allele cells.

Sequencing

Primary Analysis 
These tools convert the images gathered during Data Collection into all four colors, representing the four corresponding nucleotide bases (Figure 1). For example, our Sequence Analysis Software is a primary analysis tool that must be used after collection is completed. The Sequence Analysis software application allows users to basecall and re-basecall, trim data ends, display, edit and print sample files.

The selected basecaller processes the fluorescence signals, then assigns a base to each peak (A, C, G, T, or N). If the KB™ basecaller is used, it also provides per-base quality value predictions, optional mixed base calling, and automatic identification of failed samples (Figure 1).

Secondary Analysis
These tools allow you to further refine your results. Algorithms in our secondary analysis software products perform a number of functions supporting applications such as mutation detection and genotyping, and produce graphical outputs.

Product Selection Guide: Data Analysis Software for Sequencing

Software	Type	Features	Applications
Sequencing Analysis Software v5.4 with KB™ Basecaller v1.4.1	Primary Analysis Tool	Longer read lengths, including accuracy at 5' end Low signal to noise Basecalling quality values Enables accurate mixed basecalls	De novo Sequencing
Sequence Scanner Software v1.0	Software Viewing Tool	Review traces in thumbnail format and sort by trace quality Effective quality metrics Simultaneously view raw and analyzed data Results at a glance with Plate Report view	De novo Sequencing Quality Control
SeqScape® Software for Mutation Profiling v2.7	Secondary Analysis Tool	Obtain quality values for each base pair, consensus sequence and mutation Automatically process raw data and generate reports with mutations linked to source electropherograms Pre-configure templates Custom data views	Resequencing Medical sequencing SNP/Mutation detection SNP/Mutation/Pathogen subtyping
Variant Reporter® Software v1.1	Secondary Analysis Tool	Handle > 10 times more sample files than competing software products Accelerate data review Simple to learn Robust data filtering w/ effective quality metrics	Resequencing Comparative sequencing and direct sequencing Medical sequencing SNP/Mutation Detection

Fragment Analysis

Amplified fragments, along with appropriate size standards, migrate through a polymer-filled capillary and are detected using Data Collection Software (DCS). During an electrophoresis run, the DCS records the fluorescence intensity as a function of time and wavelength from regions on a CCD camera that correspond to different detection wavelength ranges. The resulting peaks are then processed according to the user-specified analysis parameters and size standard definition in the primary and secondary analysis software.

Primary Analysis
These tools convert the images gathered during Data Collection into sized fragment length peaks (Figure 2). For example, our Peak Scanner Software is a primary analysis tool that can be used after data collection is completed. The Peak Scanner software application allows users to size, display, edit and print sample files. Primary analysis software processes the raw data in an *.fsa file using algorithms and applies user-specified analysis settings to the results.

Secondary Analysis
These tools allow you to further refine your results. GeneMapper® Software is a flexible fragment analysis software package that provides quality DNA sizing and allele calls for all Applied Biosystems Genetic Analyzers. This software is designed to support multi-application functionality, including analysis of fragment length and/or number polymorphism applications, relative fluorescence quantitation applications, microsatellite and SNP genotyping applications, and conformation polymorphism applications. In addition to the functionality in primary analysis, our secondary analysis software (GeneMapper software) also performs a number of functions including allele calling and report table generation (Figure 3).

Product Selection Guide: Data Analysis Software for Fragment Analysis

Software	Type	Features	Applications
Peak Scanner v1.0	Primary Analysis Tool	Quickly analyze samples with the default sizing methods View or print thumbnail and checkerboard view View raw and analyzed data simultaneously Analyze large fragments (e.g. 1200 bp) View, edit, analyze, print, and export fragment analysis data	Fragment Analysis Applications
GeneMapper® Software v4.1	Primary and Secondary Analysis Tool	Security and audit features to help users meet 21 CFR Part 11 requirements Report Manager tools for customized report generation Definition of a linearity range in the analysis methods Multiuser, client-server deployment Ability to record and reapply the Size Standard Normalization factor calculated in 3500 Data Collection Analysis of six-dye data from the Applied Biosystems® 3500 and 3500xL Series systems Remote autoanalysis and command line operation Process Quality Values (PQVs) for automated evaluation Customization of the project autosaving frequency	Fragment Length/Number Polymorphism analysis Large fragment analysis Microsatellite/STR genotyping Conformation analysis Relative Fluorescence Quantitation analysis SNP genotyping Human identification for non-forensic use Other applications, such as DNA Footprinting

Next Generation Technology

A History of Innovation in Genetic Analysis (PDF)