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Pooling multiple samples increases the efficiency and lowers the cost of DNA sequencing. One approach to multiplexing is to use short DNA indices to uniquely identify each sample. After sequencing, reads must be assigned in silico to the sample of origin, a process referred to as demultiplexing.
(Renaudet al., 2015) deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics.