So far, we have focused our discussion on the analysis of genotype data. However, it is also clear that genome sequencing technologies are improving extremely rapidly. While the first two human whole genome assemblies took years to complete (49, 107), several additional genomes have been assembled just in the past 18 months (7, 57, 110). Many of the advances in whole genome sequencing have been the result of the deployment of massive throughput sequencing technologies. These technologies differ from standard Sanger based sequencing (88) in many ways. For example, the data produced by these new technologies typically has somewhat higher error rates (on the order of 1% per base). Since these technologies produce very large amounts of data, one typically accommodates these error rates by re-sequencing every base of interest many times to achieve a high-quality consensus.
