Insert size distributions differed between the sample libraries prepared for the NimbleGen and Agilent exome capture kits. Sample libraries were produced independently and were prepared according to the manufacturer's guidelines. The insert size distributions were generated based on properly mapped and paired reads determined by our capture analysis pipeline. The NimbleGen library preparation process involved agarose gel electrophoresis-based size selection, whereas the Agilent process involved a more relaxed, bead-based size selection using AMPure XP (Beckman Coulter Genomics). Bead-based size selection is useful for removing DNA fragments smaller than 100 bp but less effective than gel-based size selection in producing narrow size distributions. Yet, from a technical standpoint, the gel-based process is more susceptible to variability of mean insert size. The two different size selection processes are illustrated by our group of NimbleGen capture libraries and our group of Agilent capture libraries. PDF, probability distribution function.
Parla et al. Genome Biology 2011 12:R97 doi:10.1186/gb-2011-12-9-r97