Labeling and sample preparation for sequencing

A method for preparing nucleic acid for analysis, the method comprising the steps of:

• fragmenting nucleic acid molecules from a sample into long fragments comprising a length in a range of 5 kilobases-100 kilobases and short fragments comprising a length in a range of 100 bases-1000 bases;
• attaching an adaptor to each of 3′ and 5′ ends of the short fragments;
• hybridizing a plurality of the short fragments from the sample to individual long fragments from the sample to form a plurality of fragment complexes;
• compartmentalizing the fragment complexes in droplets with a primer pair species complementary to adaptors attached to the short fragments, wherein each droplet comprises one fragment complex and the primer pair species comprises a barcode;
• and
• amplifying the short fragments from the fragment complex in each droplet using the primer pair species.