Question: Can I use Supernova to assemble a polyploid or haploid genome?
Answer: Supernova has only been tested in-house on diploid genomes, and only on germ line samples. Haploid genomes should be fine, but have not been tested by us. We do not know if results for polyploid genomes will be satisfactory, and indeed this may depend on detailed sample characteristics (e.g. similarity between homeologs). We have not tested cancer samples.
For more information please see Achieving Success with De Novo Assembly.