The GS Amplicon Variant Analyzer (AVA) software includes a Command Line Interface (CLI) that allows the user to carry out various functions batch-wise, e.g. on various objects simultaneously and/or with multiple tasks queued through a script (described in section 3.5.15). This can afford the user substantial time savings compared with entering all data and carrying out all actions one at a time via the Graphical User Interface (GUI).

The AVA-CLI is accessed via a command interpreter called “doAmplicon”. The CLI has a flexible interface and depending on how it is invoked, you can either execute individual commands directly on the command line, read in a list of commands via a script file or a pipe, or type in commands manually in an interactive shell (see section 3.3.2.1 for the full usage statement for the doAmplicon command interpreter). The command language for the interpreter allows you to set up, manage, and compute Projects and trigger result reports (see section 3.4 for the full command language documentation).