de novo assembly applications
You can try Velvet, but you'll likely end up with thousands of contigs unless your expected reference genome is pretty simple. This question hits many of the difficulties with de novo assembly. I'm also not sure what you mean by this:


  BTW, in the Geneious I've used a FASTA file for my sequence where my '0' and '1' translated to 'C' and 'D'


Are you trying to use this for a purpose other than actual genome assembly? You say you're from the data security field, so it's unclear what's your end goal. If you only have a binary sequence, you better have a really long read length and hope there aren't too many repeats or you'll really have issues finding a consensus sequence.