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 in a transposome into first fragments derived from the target nucleic acid while the transposome is in solution, wherein the insertion sequence comprises a hybridization sequence, and wherein the transposing produces nicks in the first fragments and 3′ hydroxyl at said nicks;
• (b) combining in a single vessel or 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, said capture oligonucleotides comprising
• 1) A barcode-containing sequence, wherein the capture oligonucleotides immobilized on the same individual bead comprise the same barcode-containing sequence and a majority of beads have different barcode-containing sequences,
• 2) A common sequence complementary to at least a portion of the splint oligonucleotide, where a second portion of the splint oligonucleotide is complementary to at least a portion of the hybridization sequence;
• (c) ligating capture oligonucleotides of individual beads to inserted hybridization sequences of individual first fragments;
• and
• (d) ligating a 3′ branch ligation adaptor oligonucleotide to the first fragments at the nicks via a 3′ branch ligation, wherein 3′ branch ligation adaptor oligonucleotide is a blunt end adaptor and 3′ branch ligation comprises joining of 5′ phosphate from the blunt-end adapter covalently to the 3′ hydroxyl at the nicks of the first fragments.