A method for sequencing a region of interest, the method comprising: labeling each of a plurality of double stranded nucleic acid molecules with a barcode X and a reverse complement of the barcode X' by ligating double-stranded Y-adapters comprising universal primer binding sites and the barcodes X and X' onto the plurality of double-stranded nucleic acid molecules, wherein each barcode X is a unique molecular identifier such that each barcode X with its X' is a double stranded unique molecular identifier, and wherein each double stranded nucleic acid molecule has the double-stranded Y-adapters ligated at both ends; denaturing the plurality of double stranded nucleic acid molecules to yield single stranded target nucleic acids; amplifying the single stranded target nucleic acids using first and second probe-dependent primers, each comprising a target probe linked to a universal primer, wherein the target probe hybridizes to a target portion of the target nucleic acids and is blocked from extension and wherein the universal primer is complimentary to a universal priming site in the stem portion of the ligated Y-adaptor, to generate a plurality of amplified fragments including copies from a sense molecule of the double stranded molecules and indistinguishable second copies of a reverse complement of the sense molecule; sequencing the amplified fragments to generate sequences; aggregating the sequences of the copies and the second copies; and comparing the aggregated sequences of the copies and the second copies to make a consensus sequence, wherein the barcodes are downstream of the universal priming site on a stem portion of the adaptor. labeling each of a plurality of double stranded nucleic acid molecules with a barcode X and a reverse complement of the barcode X' by ligating double-stranded Y-adapters comprising universal primer binding sites and the barcodes X and X' onto the plurality of double-stranded nucleic acid molecules, wherein each barcode X is a unique molecular identifier such that each barcode X with its X' is a double stranded unique molecular identifier, and wherein each double stranded nucleic acid molecule has the double-stranded Y-adapters ligated at both ends; denaturing the plurality of double stranded nucleic acid molecules to yield single stranded target nucleic acids; amplifying the single stranded target nucleic acids using first and second probe-dependent primers, each comprising a target probe linked to a universal primer, wherein the target probe hybridizes to a target portion of the target nucleic acids and is blocked from extension and wherein the universal primer is complimentary to a universal priming site in the stem portion of the ligated Y-adaptor, to generate a plurality of amplified fragments including copies from a sense molecule of the double stranded molecules and indistinguishable second copies of a reverse complement of the sense molecule; sequencing the amplified fragments to generate sequences; aggregating the sequences of the copies and the second copies; and comparing the aggregated sequences of the copies and the second copies to make a consensus sequence, wherein the barcodes are downstream of the universal priming site on a stem portion of the adaptor.