Linking sequence reads using paired code tags

1. A method for preparing a library of template nucleic acids comprising:

(a) contacting a target nucleic acid with a plurality of transposons under conditions such that a portion of the plurality of transposons are inserted into the target nucleic acid, wherein at least one transposon of the plurality of transposons comprises:

a double-stranded first transposase recognition site;

a double-stranded second transposase recognition site;

a barcode disposed therebetween, wherein the barcode comprises:

a first barcode sequence of the at least one transposon;

a second barcode sequence of the at least one transposon; and

a linker disposed between the first and second barcode sequences, wherein the linker comprises a first primer site, a second primer site and a non-amplifiable site disposed between the first and second primer sites; and

(b) amplifying said target nucleic acid using one or both of the first primer site and the second primer site to separate the first barcode sequence from the second barcode sequence.

2. The method of claim 1 , wherein the target nucleic acid comprises cDNAs from a single cell.

3. The method of claim 1 , wherein the target nucleic acid comprises nucleic acids from a plurality of species.

4. The method of claim 1 , wherein the target nucleic acid comprises nucleic acids from a plurality of haplotypes.

5. The method of claim 1 , wherein the amplifying comprises contacting the target nucleic acid with a polymerase.

6. The method of claim 5 , wherein the polymerase has 3′ to 5′ exonuclease activity.

7. The method of claim 1 , wherein the first barcode sequence is on a first nucleic acid fragment comprising a first host sequence and wherein the second the barcode sequence is on a second nucleic acid fragment comprising a second host sequence.

8. The method of claim 7 , wherein the first host sequence and the second host sequence are adjacent sequences in the target nucleic acid.

9. The method of claim 1 , wherein both the first strand barcode sequence and the second strand barcode sequence are at least four nucleotides in length.

10. The method of claim 1 , wherein the amplifying comprises hybridizing a first primer to the first primer site and a second primer to the second primer site.

11. The method of claim 1 , wherein the non-amplifiable site comprises at least one nucleotide analogue.

12. The method of claim 11 , wherein the at least one nucleotide analogue does not basepair with A, C, G or T.

13. A method for preparing a library of template nucleic acids, comprising:

(a) contacting a target nucleic acid with a plurality of transposons under conditions such that a portion of the plurality of transposons are inserted into the target nucleic acid, wherein at least one transposon of the plurality of transposons comprises:

a double-stranded first transposase recognition site;

a double-stranded second transposase recognition site

a barcode disposed therebetween, wherein the barcode comprises:

a first barcode sequence of the at least one transposon;

a second barcode sequence of the at least one transposon; and

a linker disposed between the first and second barcode sequences, wherein the linker comprises a first primer site, a second primer site and a non-amplifiable site disposed between the first and second primer sites,

(b) hybridizing a primer to the first primer site; and

(c) amplifying a portion of the at least one transposon.

14. A method of analyzing a target nucleic acid comprising:

contacting a target nucleic acid with a plurality of transposons under conditions such that a portion of the plurality of transposons are inserted into the target nucleic acid to prepare the target nucleic acid for sequencing, wherein at least one transposon of the plurality of transposons comprises:

a double-stranded first transposase recognition site;

a double-stranded second transposase recognition site; and

a barcode disposed therebetween, wherein the barcode comprises:

a first barcode sequence of the at least one transposon;

a second barcode sequence of the at least one transposon; and

a linker disposed between the first and second barcode sequences, wherein the

linker comprises a first primer site, a second primer site and a non-amplifiable

site disposed between the first and second primer sites;

hybridizing a primer to the first primer site;

amplifying a portion of the at least one transposon to generate fragments of the target nucleic acid comprising the first barcode;

obtaining sequence data from the fragments of the target nucleic acid including the portion of the at least one transposon comprising the first barcode; and

assembling a representation of the target nucleic acid from the sequence data based on the first barcode sequence.

15. The method of claim 14 , further comprising hybridizing a primer to the second primer site;

amplifying a portion of the at least one transposon to generate fragments of the target nucleic acid comprising the second barcode;

obtaining sequence data from the fragments of the target nucleic acid including the portion of the at least one transposon comprising the second barcode; and

assembling a representation of the target nucleic acid from the sequence data based on the second barcode sequence, wherein the assembling comprises aligning sequence data of sequence reads having associated barcodes, wherein the associated barcodes are associated by being part of a same first barcode or second barcode before the fragments are generated.

16. The method of claim 15 , wherein the assembling comprises identifying a first barcode in one sequencing read and a paired second barcode of the first barcode in another sequencing read of the sequence data, thereby indicating proximity between the two sequencing reads in the target nucleic acid.

17. The method of claim 16 , wherein obtaining sequence data is terminated prior to obtaining sequence data from all fragments of the nucleic acid.