A method of generating a nucleotide sequence of a DNA template from DNA from a cell, the method comprising: (a) contacting the DNA with a transposase that cleaves DNA in the DNA sample to form DNA fragments and introduces adaptor sequences to ends of the DNA fragments, to form adaptor-modified DNA fragments; (b) partitioning the adaptor-modified DNA fragments into a plurality of partitions, the partitions comprising a particle comprising a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a barcode sequence and wherein different particles are distinguished by having different barcodes from one another, wherein at least some partitions have more than one particles per partition, and wherein different particles are conjugated to primers having different barcode sequences; (c) in the partitions, amplifying the adaptor-modified DNA fragments to form adaptor-modified DNA fragment amplicons and linking oligonucleotide primers from the solid support to the adaptor-modified DNA fragment amplicons, thereby forming barcoded adaptor-modified DNA fragment amplicons; (d) combining barcoded adaptor-modified DNA fragment amplicons from multiple partitions; (e) generating a plurality of sequencing reads of the barcoded adaptor-modified DNA fragment amplicons; (f) determining in a pairwise manner percent of sequencing reads of identical DNA fragments sequences shared between different barcodes; (g) comparing the determined percent of identical DNA fragment sequences shared between different barcodes to a threshold value, wherein if two barcodes have a determined percent of identical DNA fragment sequences in common above the threshold value, the two barcodes are determined to be in the same partition; and (h) generating a nucleotide sequence for the DNA template from the plurality of sequencing reads, wherein generating the nucleotide sequence comprises treating sequencing reads having different barcodes determined to be in the same partition as being from the same partition; thereby generating a nucleotide sequence of a DNA template. (a) contacting the DNA with a transposase that cleaves DNA in the DNA sample to form DNA fragments and introduces adaptor sequences to ends of the DNA fragments, to form adaptor-modified DNA fragments; (b) partitioning the adaptor-modified DNA fragments into a plurality of partitions, the partitions comprising a particle comprising a solid support surface, the solid support surface having a plurality of oligonucleotide primers conjugated thereon, wherein the oligonucleotide primers comprise a barcode sequence and wherein different particles are distinguished by having different barcodes from one another, wherein at least some partitions have more than one particles per partition, and wherein different particles are conjugated to primers having different barcode sequences; (c) in the partitions, amplifying the adaptor-modified DNA fragments to form adaptor-modified DNA fragment amplicons and linking oligonucleotide primers from the solid support to the adaptor-modified DNA fragment amplicons, thereby forming barcoded adaptor-modified DNA fragment amplicons; (d) combining barcoded adaptor-modified DNA fragment amplicons from multiple partitions; (e) generating a plurality of sequencing reads of the barcoded adaptor-modified DNA fragment amplicons; (f) determining in a pairwise manner percent of sequencing reads of identical DNA fragments sequences shared between different barcodes; (g) comparing the determined percent of identical DNA fragment sequences shared between different barcodes to a threshold value, wherein if two barcodes have a determined percent of identical DNA fragment sequences in common above the threshold value, the two barcodes are determined to be in the same partition; and (h) generating a nucleotide sequence for the DNA template from the plurality of sequencing reads, wherein generating the nucleotide sequence comprises treating sequencing reads having different barcodes determined to be in the same partition as being from the same partition; thereby generating a nucleotide sequence of a DNA template.