GS Amplicon Variant Analyzer Application

1. GS Amplicon Variant Analyzer Application

1.	GS Amplicon Variant Analyzer Application

1.1 Introduction to the GS Amplicon Variant Analyzer Application

1.2 The Overview Tab

1.3 The Project Tab

1.4 The Computations Tab

1.5 The Variants Tab

1.6 The Global Align Tab

1.7 The Consensus Align Tab

1.8 The Flowgrams Tab

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This section describes the GS Amplicon Variant Analyzer (AVA) application through its Graphical User Interface (GUI). The AVA software also features a Command Line Interface (CLI) that may be more appropriate for large Projects, especially when large amounts of data need to be imported into, exported from, or automated within a Project. See section 3 for a full description of the CLI, the language that was developed for it, and all the commands it includes.

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Projects are compatible with each other regardless of whether they are set up or computed using the Graphical User Interface (GUI) or the Command Line Interface (CLI). For certain projects, some may find it useful to set up portions of the project definition using the CLI and then enter the GUI for all subsequent tasks.

The sequencing results of Amplicon libraries are designed primarily to identify and quantitate both known and novel DNA variants (e.g. rare alleles) by the Ultra Deep Sequencing coverage of one or more region(s) of interest. This is supported by the “GS Amplicon Variant Analyzer” (AVA) software described in this section.

Briefly, the AVA application computes the alignment of reads from Amplicon libraries obtained on the GS Junior or GS FLX+ Instrument, and identifies differences between the reads and a reference sequence. Variations are displayed both graphically with a histogram indicating positions of variation, and textually with a color-coded multiple alignment that emphasizes regions and bases of difference from the reference sequence.

The software specifically reports the frequency of user-defined and software-identified variants in a summary Table, allowing for the high-throughput detection and quantitation of known and putative variants in the samples sequenced. In addition, various tools and views allow the user to examine the read alignments in detail to assess whether the software-identified variants appear to be legitimate, and possibly identify new ones. The user can then define these new variants into the system, and decide which variants to include in the analysis for quantitative reports.