A method for amplifying target nucleic acids in a nucleic acid sample, comprising: (a) extending each of a plurality of barcode primers (BC primers) to obtain extension products using the target nucleic acids as templates, wherein (i) each barcode primer comprises, from 5' to 3', a 1 st universal primer sequence, a molecular tag sequence, and a 1 st target-specific sequence, (ii) a plurality of barcode primers comprise at least 20 different barcode primers, and (iii) among the plurality of barcode primers (BC primers), the 1 st universal primer sequences are the same, but the 1 st target-specific sequences are different; wherein step (a) is limited to just one cycle; (b) separating the plurality of barcode primers that have not been extended in step (a) from the extension products; and (c) amplifying the extension products of step (b) in the presence of a plurality of limited amplification primers (LA primers) to obtain a plurality of 1 st amplification products comprising US1 at one end and US2 at the other end, wherein (i) each limited amplification primer comprises, from 5' to 3', a 2 nd universal primer sequence and a 2 nd target-specific sequence, and (ii) among the plurality of limited amplification primers, the 2 nd universal primer sequences are the same, but the 2 nd target-specific sequences are different. (a) extending each of a plurality of barcode primers (BC primers) to obtain extension products using the target nucleic acids as templates, wherein (i) each barcode primer comprises, from 5' to 3', a 1 st universal primer sequence, a molecular tag sequence, and a 1 st target-specific sequence, (ii) a plurality of barcode primers comprise at least 20 different barcode primers, and (iii) among the plurality of barcode primers (BC primers), the 1 st universal primer sequences are the same, but the 1 st target-specific sequences are different; wherein step (a) is limited to just one cycle; (i) each barcode primer comprises, from 5' to 3', a 1 st universal primer sequence, a molecular tag sequence, and a 1 st target-specific sequence, (ii) a plurality of barcode primers comprise at least 20 different barcode primers, and (iii) among the plurality of barcode primers (BC primers), the 1 st universal primer sequences are the same, but the 1 st target-specific sequences are different; (b) separating the plurality of barcode primers that have not been extended in step (a) from the extension products; and (c) amplifying the extension products of step (b) in the presence of a plurality of limited amplification primers (LA primers) to obtain a plurality of 1 st amplification products comprising US1 at one end and US2 at the other end, wherein (i) each limited amplification primer comprises, from 5' to 3', a 2 nd universal primer sequence and a 2 nd target-specific sequence, and (ii) among the plurality of limited amplification primers, the 2 nd universal primer sequences are the same, but the 2 nd target-specific sequences are different. (i) each limited amplification primer comprises, from 5' to 3', a 2 nd universal primer sequence and a 2 nd target-specific sequence, and (ii) among the plurality of limited amplification primers, the 2 nd universal primer sequences are the same, but the 2 nd target-specific sequences are different.