Digital microfluidic biochip (DMFB) is modernizing many areas of Microelectronics, Biochemistry, and Biomedical sciences. As a substitute for laboratory experiments, it is also widely known as 'lab-on-a-chip' (LOC). Minimization in pin count and avoiding cross-contamination are some of the important design issues for realistic relevance. These days, due to urgent situation and cost efficacy, more than one assay operations are essential to be carried out at the same time. So, parallelism is inevitable in DMFB. Having an area of a given chip as a constraint, how efficiently we can use a limited sized chip and how much parallelism can be incorporated are the objectives of this paper. The paper presents a design automation flow that enhances parallelism by adopting Connect-5 structure of pin configuration and considering cross-contamination problem as well. The algorithm developed in this paper assumes array-based partitioning of modules as pin-constrained design technique, where a constant number of pins have been used for desired scheduling of reagent and sample droplets. To avoid cross-contamination and at the same time to minimize the delay required for washing, wash droplet scheduling and proper placement of modules to minimize wash operations are also taken care of. © Springer India 2015.