I will soon be receiving Epstein-Barr virus sequence data, with > 800x coverage. There's a nice paper that compares de novo assembly tools (Zhang W, Chen J, Yang Y, Tang Y, Shang J, et al. (2011) A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies. PLoS ONE 6(3): e17915. doi:10.1371/journal.pone.0017915). Based on this paper, I'm thinking of using Edena as a de novo assembly tool, although other tools seem to be good as well (see figure 6 of paper).
My question is, I would like to compare the de novo assembly with a reference based one. Which reference based aligner do you recommend for a virus?