An automated system for multi-assay processing, the system comprising: a sample processing unit, a nucleic acid amplification/analysis unit, and a processor, wherein the processor is configured to cause the SPU to: a) prepare an SPU cartridge for a plurality of different target nucleic acid detection assays; b) process each SPU cartridge loaded with a plurality of samples to isolate a sample nucleic acid for each of the plurality of assays, wherein the processor is configured to cause the SPU to perform steps a) and b) using a common lockstep protocol that includes a delay step within the sample processing step or between the sample processing step and a next step of the protocol; wherein the processor is also configured to cause the nucleic acid amplification/analysis unit to: c) amplify and analyze each sample nucleic acid for a target nucleic acid specific to each of the plurality of different target nucleic acid detection assays, wherein said amplifying and analyzing includes a common lockstep protocol that includes a delay step within a nucleic acid amplification/analysis step or between a nucleic acid amplification/analysis step and a next step of the protocol; wherein the processor is configured to cause the SPU and the nucleic acid amplification/analysis unit to perform each of steps a) through c) for a time period that is equal for the plurality of different target nucleic acid detection assays, wherein the delay steps to be introduced between the assay steps of the protocols are determined before initiation of the steps a) through c), and wherein the processor is also configured to cause the nucleic acid amplification/analysis unit to initiate amplification of each sample nucleic acid at essentially the same time; whereby the delay steps eliminate resource contention. wherein the processor is configured to cause the SPU to: a) prepare an SPU cartridge for a plurality of different target nucleic acid detection assays; b) process each SPU cartridge loaded with a plurality of samples to isolate a sample nucleic acid for each of the plurality of assays, a) prepare an SPU cartridge for a plurality of different target nucleic acid detection assays; b) process each SPU cartridge loaded with a plurality of samples to isolate a sample nucleic acid for each of the plurality of assays, wherein the processor is configured to cause the SPU to perform steps a) and b) using a common lockstep protocol that includes a delay step within the sample processing step or between the sample processing step and a next step of the protocol; wherein the processor is also configured to cause the nucleic acid amplification/analysis unit to: c) amplify and analyze each sample nucleic acid for a target nucleic acid specific to each of the plurality of different target nucleic acid detection assays, wherein said amplifying and analyzing includes a common lockstep protocol that includes a delay step within a nucleic acid amplification/analysis step or between a nucleic acid amplification/analysis step and a next step of the protocol; wherein the processor is configured to cause the SPU and the nucleic acid amplification/analysis unit to perform each of steps a) through c) for a time period that is equal for the plurality of different target nucleic acid detection assays, wherein the delay steps to be introduced between the assay steps of the protocols are determined before initiation of the steps a) through c), and wherein the processor is also configured to cause the nucleic acid amplification/analysis unit to initiate amplification of each sample nucleic acid at essentially the same time; whereby the delay steps eliminate resource contention.