2. Example Amplicon Project Design and Analysis
2.
Example Amplicon Project Design and Analysis
2.1 Experimental Design
2.2 Project Setup in the AVA Software
2.3 Analysis of Known Variants
2.4 Mining a Project for New Variants
2.5 Important Factors in the Assessment of New Variants
2.6 Other Issues of Special Interest
To help better guide the reader through the process of an Amplicon Sequencing experiment, this section provides a fictitious example of the whole procedure, starting with setting the objectives and including the design of the Amplicon libraries, sequencing, and the full analysis of the results through the determination of the frequency of previously known as well as novel Variants observed in the Sample. Emphasis, however, will be on software.
This example describes a Project that does not make use of MIDs or Multiplexers. For an example of how these features are used in an Amplicon Project (using the CLI), see section
3.6
.
