Uniformity plots of exome capture data revealed fundamental differences in uniformity of target coverage between exome capture platforms. The numbers of platform-specific target bases covered from 0× to 300× depth coverage are plotted for NimbleGen (NM) and Agilent (AG) exome captures. The NimbleGen exome data were more efficient at covering the majority of intended target bases, but the corresponding uniformity plots from these data revealed that there was also some over-sequencing of these positions, which thus broadened the coverage distribution for the NimbleGen targets. The Agilent exome data, however, showed significantly more target bases with no coverage or very poor coverage compared to the NimbleGen data, thus indicating that the Agilent data provided less uniform target coverage than the NimbleGen data. The lower uniformity of coverage produced from the Agilent captures results in the need to provide more raw sequence data in order to generate adequate coverage of targets. The Agilent platform was thus less efficient at target capture than the NimbleGen platform.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97