There are many different ways to use the AVA-CLI to create or perform computations on a project. These include running doAmplicon in interactive mode, typing commands individually, using a program to automatically generate a script that can be piped into the doAmplicon command, or manually authoring a script file and invoking doAmplicon to execute the commands in that file. The command line syntax for these different options are specified in section 3.3.2.1.

This section provides examples of ways one can piece together a script of commands for setting up a Project. This example Project uses the same underlying data as the example discussed in section 2. The differences for this particular example are that a separate Reference Sequence is being entered for each EGFR exon (rather than stitching them together as an artificial reference); and that all four Read Data files are being utilized (rather than just the region 3 file). Since the sections below often digress to illustrate the variety of commands available to accomplish a specific task, they are not meant to be followed as literal step-by-step instructions for Project creation. However, section 3.5.15 presents an integrated script that can be supplied to the doAmplicon command to perform the entire example Project setup, computation and processing (provided you have access to the same sff files and you edit the paths appropriately so the script can find them).