Within each contig, sequencing errors are simulated based on the size of the contig, and whether the base position is at an end (first or last 100 bases) or in the middle of the contig. For long, double-stranded DNA viruses (e.g. variola) and bacteria, the sequencing error rates are larger at the beginning and end of a contig than in the middle, and small contigs are more likely to contain sequencing errors than are large contigs. In contrast, due to differences in generating the products for Sanger sequencing that are employed for smaller RNA and DNA viruses, there are often more sequencing errors in the middle of contigs for such smaller viral draft genomes. Although we did not specifically simulate draft for RNA and short DNA viruses, our simulator should work with minor modification to a few parameters. Thus, there are four parameters that must be specified for simulating sequencing errors: (i) the size cutoff for small versus large contigs, (ii) the probability of errors in the middle portion of small versus large contigs, (iii) the length of the contig ends where sequencing is either less accurate (bacteria and long doublestranded DNA viruses) or more accurate (small viruses, RNA viruses) and (iv) the probability of sequencing errors at the contig ends. If there is a sequencing error at a particular base, we assumed that that base is randomly changed to one of the other three bases with equal probability. Although additional features could be added to the draft simulation tool, the stochastic features that we have incorporated capture the main features of draft sequence and produce data that are suitable for SAP analyses.