A method for analyzing a single nucleic acid sample, comprising: a. producing two or more subsets of nucleic acid molecules from the single nucleic acid sample, wherein: i. the two or more subsets comprise a first subset of nucleic acid molecules and a second subset of nucleic acid molecules, and ii. the first subset of nucleic acid molecules differ from the second subset of nucleic acid molecules by one or more features selected from genomic regions, mean GC content, mean molecular size, or any combination thereof, b. separately assaying at least two of the two or more subsets of nucleic acid molecules, wherein: i. a first assay, comprising a first sequencing reaction, is conducted on the first subset of the two or more subsets to produce a first result comprising nucleic acid sequence information generated from the first subset of nucleic acid molecules, and ii. a second assay, comprising a second sequencing reaction, is conducted on the second subset of the two or more subsets to produce a second result comprising nucleic acid sequence information generated from the second subset of nucleic acid molecules; and c. combining, with the aid of a computer processor, the first and second nucleic acid sequences from the first result and second result by means of a statistical algorithm utilizing one or more of base read quality and allele frequency to compute a consensus call at one or more applicable loci, thereby analyzing the nucleic acid sample. a. producing two or more subsets of nucleic acid molecules from the single nucleic acid sample, wherein: i. the two or more subsets comprise a first subset of nucleic acid molecules and a second subset of nucleic acid molecules, and ii. the first subset of nucleic acid molecules differ from the second subset of nucleic acid molecules by one or more features selected from genomic regions, mean GC content, mean molecular size, or any combination thereof, i. the two or more subsets comprise a first subset of nucleic acid molecules and a second subset of nucleic acid molecules, and ii. the first subset of nucleic acid molecules differ from the second subset of nucleic acid molecules by one or more features selected from genomic regions, mean GC content, mean molecular size, or any combination thereof, b. separately assaying at least two of the two or more subsets of nucleic acid molecules, wherein: i. a first assay, comprising a first sequencing reaction, is conducted on the first subset of the two or more subsets to produce a first result comprising nucleic acid sequence information generated from the first subset of nucleic acid molecules, and ii. a second assay, comprising a second sequencing reaction, is conducted on the second subset of the two or more subsets to produce a second result comprising nucleic acid sequence information generated from the second subset of nucleic acid molecules; and i. a first assay, comprising a first sequencing reaction, is conducted on the first subset of the two or more subsets to produce a first result comprising nucleic acid sequence information generated from the first subset of nucleic acid molecules, and ii. a second assay, comprising a second sequencing reaction, is conducted on the second subset of the two or more subsets to produce a second result comprising nucleic acid sequence information generated from the second subset of nucleic acid molecules; and c. combining, with the aid of a computer processor, the first and second nucleic acid sequences from the first result and second result by means of a statistical algorithm utilizing one or more of base read quality and allele frequency to compute a consensus call at one or more applicable loci, thereby analyzing the nucleic acid sample.