Different runs of the de novo assembler can result in slightly different results. This is caused by multi-threading of the program combined with the use of probabilistic data structures. If you were to run the assembler using a single thread, the effect would not be observed. That is, the same results would be produced in every run. However, an assembly run on a single thread would be very slow. The assembler should run quickly. Thus, we use multiple threads to accelerate the program.
Randomness in the results
The main reason for the assembler producing different results in each run is that threads construct contigs in an order that is correlated with the thread execution order, which we do not control. The size and "position" of a contig can change dramatically if you start building a contig from two different starting points (i.e. different words, or k-mers), which means that different assembly runs can lead to different results, depending on the order in which threads are executed. Whether a contig is scaffolded with another contig can also be affected by the order that contigs are constructed. In this case, you could see quite large differences in the lengths of some contigs reported. This will be particularly noticeable if you have an assembly with reasonably few contigs of great length.
We are working on addressing the fact that slightly different output is returned with different runs of the de novo assembler without appreciably affecting the speed of the assembler. For the moment, the output of runs may vary slightly, but the overall information content of the assembly should not be markedly different.