Illustration of the method used for gene identification in S. aureus D30 and S. aureus 930918-3. The raw sequences were assembled into contigs using Newbler with a contig size threshold of 500 bases. The raw reads that were not assembled were then aligned against individual matching genes and the assemblies were tested for completeness. Those genes that were covered over at least 90% of their length were considered present. The sum total of genes thus identified in each genome was subjected to comparative genome analysis.