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GS Amplicon Variant Analyzer Application
Introduction to the GS Amplicon Variant Analyzer Application
Launching the GS Amplicon Variant Analyzer GUI Application
GS Amplicon Variant Analyzer Application Interface Overview
The Overview Tab
The Project Tab
The “Project Tree” Sub-Tabs
The “Definition Table” Sub-Tabs
The Computations Tab
The Variants Tab
The Variants Frequency Table
Variant Data Display Controls
The Global Align Tab
Populating the Global Align Tab
The Variation Frequency Plot
The Multiple Alignment Display
Display Option Tools
The Consensus Align Tab
Populating the Consensus Align tab
The Variation Frequency Plot
The Multiple Alignment Display
Display Option Tools
The Flowgrams Tab
Populating the Flowgrams Tab
The Triflowgram Plot
Navigation on the Flowgrams Tab
Example Amplicon Project Design and Analysis
Experimental Design
Project Setup in the AVA Software
Launching the AVA Application
Creating a New Project
Defining the Reference Sequence
Defining the Amplicons
Defining the Sample
Defining the Known Variant
Importing the Read Data Set
Analysis of Known Variants
Compute the Project
Frequency of Known Variants
Mining a Project for New Variants
Important Factors in the Assessment of New Variants
Above the Noise
Coverage
Bidirectional Support
Homopolymers
Flowgram Evidence
Read Length
Other Issues of Special Interest
What Does ‘Sample’ Mean?
How Should Your Project Be Organized?
Should Amplicons Share a Reference Sequence or Have Individual Ones?
When should MIDs be used?
What is the purpose of Multiplexers?
GS Amplicon Variant Analyzer Command Line Interface
Purpose of the CLI
Data Import
Data Export
Automating the Triggering of Computations
Result Reporting
AVA-CLI Command Language Overview
Entities
Available Commands
AVA-CLI General Online Help
Help
General Help
AVA-CLI Command Usage Statements
associate
close
computation
create
dissociate
exit
list
load
open
remove
rename
report
save
set
show
update
utility
Creating and Computing a Project with the AVA-CLI
Setting CLI Parameters
Creating a New Project
Creating References
Creating Amplicons
Creating Variants
Creating Samples
Associating Samples with Amplicons
Loading Read Data Sets
Associating Read Data Sets with Samples
Editing Object Properties
Computation
Reporting
Finishing Touches
Exporting from the Project
Integrated Project Script
Creating and Computing an MID Project with the AVA-CLI
Example MID Project Script
GS Amplicon Variant Analyzer – Special Topics
Intelligent Variant Naming
Tier 1 Naming
Tier 2 Naming
Tier 3 Naming
Tier 4 Naming
Naming Example
Properties Windows for Global and Consensus Alignments
When is the Properties Information Useful?
Content of the Three “Properties” Window Types
Automatic Project Initialization in the GUI
Default Initialization Script Location
Default Initialization Script Contents
Initialization Script Restrictions
Initialization Script Error Handling
Project Initialization and the CLI
Multiplex Amplicon Libraries
Glossary