Sample preparation for Roche/454, ABI/SOLiD and Life Technologies/Ion Torrent 
sequencing are based on amplification of library fragments on the surface of 
beads prior to sequencing. Commonly, libraries are barcoded and pooled, to 
maximise the sequence output of each sequence run. Here, we describe a novel 
approach for normalization of multiplex next generation sequencing libraries 
after emulsion PCR. Briefly, amplified libraries carrying unique barcodes are 
prepared by fluorescent tagging of complementary sequences and then resolved by 
high-speed flow cytometric sorting of labeled emulsion PCR beads. The protocol 
is simple and provides an even sequence distribution of multiplex libraries when 
sequencing the flow-sorted beads. Moreover, since many empty and mixed emulsion 
PCR beads are removed, the approach gives rise to a substantial increase in 
sequence quality and mean read length, as compared to that obtained by standard 
enrichment protocols.