Single cell nucleic acid detection and analysis

A method, comprising:

• (a) tagging a population of double-stranded nucleic acid molecules, each molecule having two ends, with asymmetric sequencing adapters, each adapter having a barcode sequence, to generate a plurality of tagged nucleic acid molecules, wherein the population comprises nucleic acid molecules that differ in sequence from each other, wherein an adapter is joined to both ends of the nucleic acid molecules;
• (b) amplifying the tagged nucleic acid molecules, whereby amplicons of the tagged nucleic acid molecules are derived from individual double-stranded nucleic acid molecules from the population of double-stranded nucleic acid molecules, wherein the amplicons comprise two complementary single-stranded nucleic acid molecules;
• (c) sequencing a plurality of the amplicons to generate paired-end sequence reads derived from sequencing the complementary single-stranded nucleic acid molecules, wherein the sequence reads comprise the sequence of the amplicons and the sequence of the associated barcodes,
• (d) aligning the sequence reads to a reference sequence, wherein the starting position and ending position of the sequence of the amplicons from which the reads are derived can be determined, and wherein the aligning is performed by a computer implemented method, and
• (e) forming groups of the paired-end sequence reads that can be aligned to the same starting and ending position on the reference sequence and that have the same barcode sequences, wherein paired-end sequence reads obtained from both of the complementary single-strands are identified, and
• (f) counting the number of groups that comprise paired-end reads that can be aligned to the same starting and ending position and have the different barcode sequences.