A method for amplifying one or more target nucleic acids, the method comprising: contacting sample nucleic acids with a forward primer and a reverse primer for each target nucleic acid, wherein each primer comprises a target-specific portion and a common sequence 5' of the target-specific portion, a DNA sequencing primer binding site 5' of the common sequence, and a nucleotide tag 5' of the DNA sequencing primer binding site, wherein the first and second nucleotide tags in the forward and reverse primers are different, and wherein the common sequence comprises a transposon sequence and amplifying the target nucleic acid(s) in a first amplification to produce at least one target amplicon wherein a target nucleotide sequence is flanked by the common sequence on one end and its reverse complement on the other end, whereby a single strand of the target amplicon can form a stem loop structure, wherein the first amplification is carried out in a microfluidic device comprising a plurality of reaction chambers using a third primer, wherein the third primer comprises a portion specific for the second of the nucleotide tags, a barcode nucleotide sequence 5' of the tag-specific portion, and a first flow cell attachment site 5' of the barcode nucleotide sequence, wherein the first amplification produces first target amplicons having the structure: 5'-first nucleotide tag-first primer binding site- common sequence-target nucleotide sequence-reverse complement of common sequence-second primer binding site-second nucleotide tag-barcode nucleotide sequence-first flow cell attachment site-3'; recovering the first target amplicons from the microfluidic device after the first amplification; and amplifying the first target amplicons in a second amplification using a fourth primer having a portion specific for the first nucleotide tag and a second flow cell attachment site 5' of said first nucleotide tag-specific portion and a reverse primer specific for the first flow cell attachment site, wherein the second amplification produces second target amplicons having the structure: 5'-second flow cell attachment site-first nucleotide tag-first primer binding site- common sequence-target nucleotide sequence-reverse complement of common sequence-second primer binding site-second nucleotide tag-barcode nucleotide sequence-first flow cell attachment site-3'. contacting sample nucleic acids with a forward primer and a reverse primer for each target nucleic acid, wherein each primer comprises a target-specific portion and a common sequence 5' of the target-specific portion, a DNA sequencing primer binding site 5' of the common sequence, and a nucleotide tag 5' of the DNA sequencing primer binding site, wherein the first and second nucleotide tags in the forward and reverse primers are different, and wherein the common sequence comprises a transposon sequence and amplifying the target nucleic acid(s) in a first amplification to produce at least one target amplicon wherein a target nucleotide sequence is flanked by the common sequence on one end and its reverse complement on the other end, whereby a single strand of the target amplicon can form a stem loop structure, wherein the first amplification is carried out in a microfluidic device comprising a plurality of reaction chambers using a third primer, wherein the third primer comprises a portion specific for the second of the nucleotide tags, a barcode nucleotide sequence 5' of the tag-specific portion, and a first flow cell attachment site 5' of the barcode nucleotide sequence, wherein the first amplification produces first target amplicons having the structure: 5'-first nucleotide tag-first primer binding site- common sequence-target nucleotide sequence-reverse complement of common sequence-second primer binding site-second nucleotide tag-barcode nucleotide sequence-first flow cell attachment site-3'; recovering the first target amplicons from the microfluidic device after the first amplification; and amplifying the first target amplicons in a second amplification using a fourth primer having a portion specific for the first nucleotide tag and a second flow cell attachment site 5' of said first nucleotide tag-specific portion and a reverse primer specific for the first flow cell attachment site, wherein the second amplification produces second target amplicons having the structure: 5'-second flow cell attachment site-first nucleotide tag-first primer binding site- common sequence-target nucleotide sequence-reverse complement of common sequence-second primer binding site-second nucleotide tag-barcode nucleotide sequence-first flow cell attachment site-3'.