I am trying to process data from a bacterial genome after sequencing it using SOAPdenovo. I obtain a small number of scaffolds, and I would like, if possible, to guess their order in the genome. I happen to have the reference genome for the bacteria too, so I aligned the scaffolds to it using progressive Mauve, and they are spread over the genome. I was sort of expecting it. My question is: are there tools to guess the order when doing truly denovo assembling?