A method for preparing a sequencing library for sequencing a target nucleic acid comprising: (a) providing (i) single-stranded DNA circles of the target nucleic acid with one or more copies of unique molecular identifier and (ii) a plurality of first beads, wherein each first bead comprises a plurality of first capture oligonucleotides, wherein each first capture oligonucleotide comprises a first barcode comprising a first barcode sequence, wherein all first capture oligonucleotides immobilized on the same individual bead comprise the same first barcode sequence, and a majority of beads have different first barcode sequences, (b) amplifying the single-stranded DNA circles from (a) by rolling circle amplification to produce a plurality of single-stranded concatemers that comprise at least five copies of a single-stranded fragment, (c) converting the single-stranded concatemers into double-stranded or partially double-stranded DNA molecules, (d) introducing staggered single-stranded breaks to the DNA molecules in (c), thereby generating first complexes, each comprising a plurality of first subfragments from one of the DNA molecules in (c), (e) associating at least some of the first subfragments in the first complexes with first capture oligonucleotides immobilized on a plurality of individual first beads, wherein each individual first bead comprises a plurality of the first capture oligonucleotides, thereby providing barcoded first subfragments. (a) providing (i) single-stranded DNA circles of the target nucleic acid with one or more copies of unique molecular identifier and (ii) a plurality of first beads, wherein each first bead comprises a plurality of first capture oligonucleotides, wherein each first capture oligonucleotide comprises a first barcode comprising a first barcode sequence, wherein all first capture oligonucleotides immobilized on the same individual bead comprise the same first barcode sequence, and a majority of beads have different first barcode sequences, wherein each first bead comprises a plurality of first capture oligonucleotides, wherein each first capture oligonucleotide comprises a first barcode comprising a first barcode sequence, wherein all first capture oligonucleotides immobilized on the same individual bead comprise the same first barcode sequence, and a majority of beads have different first barcode sequences, (b) amplifying the single-stranded DNA circles from (a) by rolling circle amplification to produce a plurality of single-stranded concatemers that comprise at least five copies of a single-stranded fragment, (c) converting the single-stranded concatemers into double-stranded or partially double-stranded DNA molecules, (d) introducing staggered single-stranded breaks to the DNA molecules in (c), thereby generating first complexes, each comprising a plurality of first subfragments from one of the DNA molecules in (c), (e) associating at least some of the first subfragments in the first complexes with first capture oligonucleotides immobilized on a plurality of individual first beads, wherein each individual first bead comprises a plurality of the first capture oligonucleotides, thereby providing barcoded first subfragments.