a) obtaining segments of genomic nucleic acids from a sample containing the genomic nucleic acids;

b) randomly tagging the segments of genomic nucleic acids with different nucleic acid tags, thereby generating unique tagged nucleic acid molecules from the segments of genomic nucleic acids, such that each of the unique tagged nucleic acid molecules comprises a segment of the segments of the genomic nucleic acids from step (a) and a nucleic acid tag of the nucleic acid tags;

c) subjecting the unique tagged nucleic acid molecules to a polymerase chain reaction (PCR), thereby generating copies of the unique tagged nucleic acid molecules;

d) generating tag associated sequence reads by sequencing the copies of the unique tagged nucleic acid molecules of step (c);

e) assigning each of the unique tagged nucleic acid molecules to a location on a genome by mapping each of the tag associated sequence reads of step (d) to a location in the genome; and

f) in a plurality of locations in the genome, obtaining relative copy number information of the genomic nucleic acids from the sample based on the number of unique tagged nucleic acid molecules that have been assigned to each of the plurality of locations in the genome.