We performed six sets of analyses using simulated variola draft. Three sets of simulated variola draft runs of the SAP used the following parameters: probability of a gap between contigs ¼ 0.95; probability of overlap between contigs ¼ 0.05; minimum gap size if there is a gap (uniform distribution) ¼ 1 bp; maximum gap size ¼ 2000 bp; minimum overlap if there is overlap (uniform distribution) ¼ 20 bp; maximum overlap ¼ 40 bp; minimum contig size (exponential distribution) ¼ 2000 bp; maximum contig size ¼ 0.5 · (mean genome length) bp mean contig size ¼ 0.05 · (mean genome length) bp cutoff size for small versus large contigs ¼ 10 000 bp; probability of sequence errors inside large contigs ¼ 0.01; probability of sequence errors inside small contigs ¼ 0.05; We will refer to the above set of simulations as those with a high probability of sequencing errors, or low-quality draft. The other three simulated variola draft runs used all the same parameters as above, except that the sequencing error rates were dramatically lower, more in line with error rates of 10 À5 / base that the US Centers for Disease Control and Prevention (CDC) has indicated for their draft variola genomes: probability of sequence errors inside large contigs ¼ 10 À5 ; probability of sequence errors inside small contigs ¼ 10 À4 ; probability of sequence errors in the contig ends ¼ 10 À3 ; These runs were referred to as low error rate, or highquality draft. Finally, we performed SAP runs using high error rate (low quality) simulated draft of the NN sequences and intermediate quality simulated draft of target genomes, using the following probabilities of sequencing errors: probability of sequence errors inside large contigs ¼ 10 À3 ; probability of sequence errors inside small contigs ¼ 10 À3 ; probability of sequence errors in the contig ends ¼ 10 À3 ;