Overview of Minimus pipeline. Several independent modules of the AMOS package (shown as ovals) interact through the AMOS API to a central data-structure (called a Bank). The order of execution of the individual modules is shown by the arrow. Note that the inputs and outputs to minimus follow the AMOS file format (AMOS message files). The AMOS package provides converters between this file format and virtually all commonly used formats for representing sequence data and genome assemblies.