A method for designing sequencing barcodes that can withstand a large numberof insertion, deletion and substitution errors and are suitable for use inmultiplex single-molecule real-time sequencing is presented. The manuscriptfocuses on the design of barcodes for full-length single-pass reads, impairedby challenging error rates in the order of 11%. To the authors' knowledge, thisis the first method to specifically address this problem without requiringupstream quality improvement. The proposed barcodes can multiplex hundreds orthousands of samples while achieving sample misassignment probabilities as lowas $10^{-7}$, and are designed to be compatible with chemical constraintsimposed by the sequencing process. Software for constructing watermark barcodesets and demultiplexing barcoded reads, together with example sets of barcodesand synthetic barcoded reads, are freely available atwww.cifasis-conicet.gov.ar/ezpeleta/NS-watermark.
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