Single tube bead-based dna co-barcoding for accurate and cost-effective sequencing, haplotyping, and assembly

A method of preparing a sequencing library for sequencing a target nucleic acid without the use of nanodrops comprising:

• (a) transposing an insertion sequence into first fragments of the target nucleic acid, wherein the insertion sequence comprises a hybridization sequence, and wherein the transposing produces nicks in the first fragments, wherein optionally the target nucleic acid is not amplified prior to step (a);
• (b) combining in a single mixture (i) the first fragments of the target nucleic acid from (a), (ii) a splint oligonucleotide, and (iii) a population of beads, wherein each bead comprises capture oligonucleotides immobilized thereon, wherein optionally the capture oligos are connected to beads at the 5′ terminus end,
• wherein optionally the population of beads comprises, in aggregate, at least 100,000 different tag sequences or at least 1 million different tag sequences,
• wherein, optionally, on average, the spacing of barcoded capture oligos on the beads is <10 nm, <15 nm, <20 nm, <30 nm, <40 nm, or 50 nm
• wherein said capture oligonucleotides comprising
• 1) a tag (or barcode)-containing sequence, wherein each tag (or barcode)-containing sequence comprises a barcode sequence, which is optionally a tripartate barcode sequence, wherein the oligonucleotides immobilized on the same individual bead comprise the same tag (or barcode)-containing sequence and a majority of beads have different tag (or barcode)-sequences,
• 2) a common sequence complementary to at least a portion of a splint oligonucleotide, where a second portion of the splint oligonucleotide is complementary to at least a portion of the hybridization sequence;
• 3) optionally a first PCR primer annealing site;
• (c) ligating capture oligonucleotides of individual beads to inserted hybridization sequences of individual first fragments.