In manufacturing, rising demands for customized products have led to increased product variance and shortened product life cycles. In assembly lines, an increased variant diversity impedes the product flow. As a result, the utilization of assembly resources decreases, and production costs grow. An approach to increase the flexibility and adaptability of the assembly system is the implementation of the concept of line-less assembly. In the first step, the assembly line is dissolved. Then, stations are reallocated and linked by automated guided vehicles resulting in a loosely coupled layout, for example, a parallelization and interconnection of multiple lines or a matrix layout. A key requirement for the successful operation and control of a line-less assembly system is the collection and correct interpretation of data. To fully exploit the flexibility and adaptability of the concept of line-less assembly, a software architecture for planning and control must base on an information model allowing the fast integration of all shop floor assets and other data resources. Therefore, a modular data model with standardized interfaces for interoperable data exchange like a digital twin is needed. The aim of this paper is the development and implementation of a software architecture for planning and control of a line-less assembly system. Moreover, the architecture should integrate an interoperable digital twin of the physical system. To satisfy the criteria of interoperability and fast deployment, the digital twins are evolved following the methodology of a digital twin pipeline. Furthermore, a physical demonstrator serves as a testbed for the developed software architecture and digital twins. On the level of production planning and control, relevant industrial applications are identified and implemented in the form of use cases to show the functionality of the line-less assembly system as cyber-physical production system.