Methods for obtaining a sequence

1. A method for obtaining a sequence, the method comprising:

ligating adapters to a plurality of nucleic acid fragments in a sample, each nucleic acid fragment having a length between 5 kilobases and 40 kilobases;

quantifying the amount of nucleic acid fragments present in the sample to which adapters have been ligated on each end, thereby quantifying the amount of amplifiable nucleic acid fragments;

determining a dilution factor based on the quantified amount of amplifiable nucleic acid fragments;

partitioning the sample based on the dilution factor such that each partitioned portion comprises, on average, at least two amplifiable nucleic acid fragments that are a subset of unique sequences;

performing a polymerase chain reaction on the partitioned nucleic acid fragments;

sequencing the nucleic acid fragments to obtain sequence reads; and

obtaining a sequence from the reads.

2. The method according to claim 1 , wherein prior to the ligating step, the method further comprises fragmenting nucleic acid.

3. The method according to claim 2 , wherein the adapters comprise unique marker identifiers.

4. The method according to claim 3 , wherein the unique marker identifiers comprise bar code sequences that are part of adapter sequences.

5. The method according to claim 4 , wherein the bar code sequences in the adapters attached to both ends of a fragment are the same or different.

6. The method according to claim 4 , wherein the adapter sequences are amplification adapters.

7. The method according to claim 3 , further comprising attaching labels to the nucleic acid fragments in each partitioned portion.

8. The method according to claim 7 , wherein the attaching labels step is performed after the polymerase chain reaction.

9. The method according to claim 8 , wherein after the polymerase chain reaction, the method further comprises fragmenting the amplified nucleic acids in each partitioned portion.

10. The method according to claim 1 , wherein partitioning comprises dispensing the sample into different wells of a microwell plate.

11. The method according to claim 1 , wherein partitioning comprises segmenting the sample into droplets.

12. The method according to claim 1 , wherein the sequence is a consensus sequence or a haplotype sequence.

13. A method for obtaining a sequence, the method comprising:

obtaining nucleic acid;

fragmenting the nucleic acid, thereby generating nucleic acid fragments that have a length of 5 kilobases to 40 kilobases;

ligating adapters to a portion of the nucleic acid fragments, wherein the portion of nucleic acid fragments with adapters ligated at each end are amplifiable nucleic acid fragments;

quantifying an amount of the amplifiable nucleic acid fragments present in the sample;

determining a dilution factor based on the quantified amount of amplifiable nucleic acid fragments;

partitioning the nucleic acid fragments based on the dilution factor, wherein each partitioned portion comprises, on average, at least two amplifiable nucleic acid fragments that are a subset of unique sequences;

amplifying the partitioned nucleic acid fragments by performing a polymerase chain reaction;

attaching bar codes to the amplified nucleic acid fragments;

sequencing the nucleic acid fragments to obtain bar coded sequence reads; and

obtaining a sequence from the reads.

14. The method according to claim 13 , wherein each adapter comprises a marker identifiers.

15. The method according to claim 13 , wherein partitioning comprises dispensing the sample into different wells of a microwell plate.

16. The method according to claim 13 , wherein partitioning comprises segmenting the sample into droplets.

17. The method according to claim 13 , wherein the sequence is a consensus sequence or a haplotype sequence.