Identification of nucleic acid template-linked barcodes comprising nucleic acid modifications

A method of identifying a barcode, the method comprising:

• a) providing a sequencing template comprising a nucleic acid linked to a barcode, wherein the barcode consists of a nucleotide sequence comprising a base modification;
• b) subjecting the sequencing template to a single-molecule sequencing reaction;
• c) collecting reaction data in real time during the single-molecule sequencing reaction, wherein said reaction data comprises a sequence read for the sequencing template, and wherein the reaction data further comprises a kinetic change in the single-molecule sequencing reaction, wherein the kinetic change is indicative of the base modification in the nucleotide sequence of the barcode;
• and
• d) analyzing both the sequence read and the kinetic change in the reaction data to detect the nucleotide sequence of the barcode, thereby identifying the barcode in the sequencing template.