A method of whole genome sequencing of a single cell or cell-group for identification of single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group, the method comprising: i) providing a multi-well array plate comprising rows and columns of reaction wells; ii) providing genomic DNA of single cells or cell-groups, wherein the genomic DNA is distributed into a plurality of reaction wells on the multi-well array plate, such that there is no more than one single-stranded genomic DNA molecule of any given locus per reaction well, iii) carrying out whole genome amplification of each genomic DNA molecule to provide multiple copies of the genomic DNA molecule in each reaction well; iv) fragmenting the DNA molecules of each reaction well and ligating a pair of looped adapters at each end or tagmenting using transposase-delivered adapters to form adapted-DNA fragments, wherein the looped adapters or transposase-delivered adapters comprise either a Column Index (Ci) sequence or a Row Index (Ri) sequence, wherein the Ci sequence is common to each looped adapter or transposase-delivered adapter of every reaction well in a column of the multi-well array plate, or wherein each Ri sequence is common to each looped adapter or transposase-delivered adapter of every reaction well in a row of the multi-well array plate; vi) providing the indexed DNA library by performing indexing PCR on the adapted-DNA fragments, wherein the adapted-DNA fragments are amplified to form indexed PCR products using forward and reverse indexing primers, wherein either a Row Index (Ri) sequence or Column Index (Ci) sequence is introduced by each forward and reverse indexing primers onto each end of the adapted-DNA fragments, such that the resulting indexed PCR products comprise both a pair of flanking Column Index (Ci) sequences that are common to each well of a column and a pair of flanking Row Index (Ri) sequences that are common to each well of a row, and vii) sequencing the indexed DNA library to provide data for determining any single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group. i) providing a multi-well array plate comprising rows and columns of reaction wells; ii) providing genomic DNA of single cells or cell-groups, wherein the genomic DNA is distributed into a plurality of reaction wells on the multi-well array plate, such that there is no more than one single-stranded genomic DNA molecule of any given locus per reaction well, iii) carrying out whole genome amplification of each genomic DNA molecule to provide multiple copies of the genomic DNA molecule in each reaction well; iv) fragmenting the DNA molecules of each reaction well and ligating a pair of looped adapters at each end or tagmenting using transposase-delivered adapters to form adapted-DNA fragments, wherein the looped adapters or transposase-delivered adapters comprise either a Column Index (Ci) sequence or a Row Index (Ri) sequence, wherein the Ci sequence is common to each looped adapter or transposase-delivered adapter of every reaction well in a column of the multi-well array plate, or wherein each Ri sequence is common to each looped adapter or transposase-delivered adapter of every reaction well in a row of the multi-well array plate; vi) providing the indexed DNA library by performing indexing PCR on the adapted-DNA fragments, wherein the adapted-DNA fragments are amplified to form indexed PCR products using forward and reverse indexing primers, wherein either a Row Index (Ri) sequence or Column Index (Ci) sequence is introduced by each forward and reverse indexing primers onto each end of the adapted-DNA fragments, such that the resulting indexed PCR products comprise both a pair of flanking Column Index (Ci) sequences that are common to each well of a column and a pair of flanking Row Index (Ri) sequences that are common to each well of a row, and vii) sequencing the indexed DNA library to provide data for determining any single nucleotide variants, determining chromosome structural variations, or determining phasing information in the genome of the single cell or cell-group.