A method of generating a nucleotide sequence of a DNA template, the method comprising: (a) partitioning a sample into a plurality of 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; (b) providing in the partitions DNA template fragments to be sequenced; and (c) in the partitions, linking oligonucleotide primers from the solid support to at least a fragment of DNA template, thereby forming barcoded DNA template fragments; combining barcoded DNA template fragments from multiple partitions; generating a plurality of sequencing reads of the barcoded DNA templates; (e) determining in a pairwise manner percent of sequencing reads of DNA template fragments shared between different barcodes; (f) comparing the determined percent of DNA template fragments shared between different barcodes to a threshold value, wherein if two barcodes have a determined percent of identical DNA template fragments in common above the threshold value, the two barcodes are determined to be in the same partition; and (g) 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) partitioning a sample into a plurality of 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; (b) providing in the partitions DNA template fragments to be sequenced; and (c) in the partitions, linking oligonucleotide primers from the solid support to at least a fragment of DNA template, thereby forming barcoded DNA template fragments; combining barcoded DNA template fragments from multiple partitions; generating a plurality of sequencing reads of the barcoded DNA templates; (e) determining in a pairwise manner percent of sequencing reads of DNA template fragments shared between different barcodes; (f) comparing the determined percent of DNA template fragments shared between different barcodes to a threshold value, wherein if two barcodes have a determined percent of identical DNA template fragments in common above the threshold value, the two barcodes are determined to be in the same partition; and (g) 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;