Over the last four years, we witnessed the tremendous advances in Next Generation Sequencing (NGS) that have dramatically decreased the cost of whole genome sequencing. However, the cost of sequencing larger genomes is still significant. In addition and depending on the goal of study, whole genome sequencing creates a large amount of additional/auxiliary data that complicates data analysis. There are several commercial methods available for isolating subsets of genomes that greatly enhance the efficiency of NGS by allowing researchers to focus on their regions of interest. For the 2009–11 DSRG study, we compared products from two leading companies; Agilent and Nimblegen, that offer custom enrichment methods. Both companies obtained the same genomic DNA stock and performed DNA capture on the same specified regions. Following capture, the Illumina Genome Analyzer IIx system was used, in two different laboratories, to generate the sequence data. We present our data comparing in terms of cost, quality, reproducibility and most importantly completeness and depth of coverage. Acknowledgements: We would like to thank Agilent, Illumina and Nimblegen for all their support in making this study possible
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