Tagging nucleic acids for sequence assembly

A method of mapping a sequence to a nucleic acid molecule, comprising the steps of:

• obtaining a nucleic acid sample comprising a first nucleic acid molecule comprising a first region and a second region;
• crosslinking said nucleic acid sample outside of a cell such that said first region and said second region of said first nucleic acid molecule are bound independently of a phosphodiester backbone of said first nucleic acid molecule;
• fragmenting said nucleic acid sample to produce at least one double strand break between said first region and said second region of said first nucleic acid molecule;
• contacting said nucleic acid sample to a population of oligonucleotides comprising a first plurality of oligonucleotides,
• wherein each of said first plurality of oligonucleotides comprises a) a 3′ annealing region capable of annealing to said double strand break, and b) a first molecular tag sequence 5′ of said 3′ annealing region, and
• wherein at least one of said first plurality of oligonucleotides anneals to one or more nucleotides on either side of said double strand break of said first nucleic acid molecule;
• ligating each side of said double strand break to at least one of said first plurality of oligonucleotides to form a ligation product;
• recovering said first nucleic acid molecule;
• and
• sequencing said ligation product;
• wherein a first sequence read comprising said first molecular tag sequence corresponds to a sequence of said first nucleic acid molecule.