Comparison of conventional and massively parallel sequence pipelines. Both pipelines begin with a DNA fragmentation step. (a) The steps in a conventional genome-sequencing pipeline, most of which require dedicated automation and processing in a 384-well format. DNA fragments are subcloned into bacterial vectors and introduced into bacterial cells to prepare a library covering the whole genome. The transformed cells containing subclones are plated and grown and then harvested by robotic picking, and the DNA from each one is isolated and sequenced. The sequence is visualized by loading onto a capillary sequencing instrument. (b) The steps in a generic massively parallel genome-sequencing pipeline. Genomic DNA fragments first undergo end repair to provide blunt ends for adaptor ligation and then have specific adaptors ligated to their ends that contain priming sites for PCR and sequencing. The adaptor-ligated fragments are then hybridized to complementary adaptors that are fixed to a surface (a slide or bead), and then in situ PCR amplification is used instead of bacterial amplification in vivo. Sequencing reactions of the surface-amplified fragments take place on the surface. The sequence is visualized using either luciferase (pyrosequencing) or fluorescence reporting that is detected by a CCD camera.