Yield output from pond library construction methods. Data are shown left to right, for pond libraries constructed with three methods: the widely used standard column-based cleanups , an automated implementation of standard bead cleanups and our implementation of with-bead SPRI cleanups. Each library was constructed with 3 μg input of NA12878 genomic DNA, in triplicate. Bars: total DNA output from pond library construction before PCR amplification. Blue diamonds: percentage recovery of input DNA for duplicates of 3 μg of the same input DNA. With-bead-based cleanups increased the amount of DNA retained throughout library construction compared to the standard column or SPRI cleanup methods.