Methods and systems for nucleic acid sequencing

1. A method for processing a plurality of nucleic acid molecules, comprising:

(a) directing a plurality of nucleotides or nucleotide analogs to a first reaction space comprising a support having a first plurality of nucleic acid molecules immobilized thereto;

(b) incorporating a subset of nucleotides or nucleotide analogs from said plurality of nucleotides or nucleotide analogs into said first plurality of nucleic acid molecules, thereby providing a remainder of said plurality of nucleotides or nucleotide analogs, wherein (b) is performed in absence of detecting said subset of nucleotides incorporated into said first plurality of nucleic acid molecules;

(c) bringing said remainder of said plurality of nucleotides or nucleotide analogs in contact with a second plurality of nucleic acid molecules in a second reaction space; and

(d) incorporating at least a subset of said remainder of said plurality of nucleotides or nucleotide analogs into said second plurality of nucleic acid molecules.

2. The method of claim 1 , further comprising detecting said at least said subset of said remainder of said plurality of nucleotides or nucleotide analogs incorporated into said second plurality of nucleic acid molecules.

3. The method of claim 1 , wherein said subset of said remainder of said plurality of nucleotides or nucleotide analogs comprises nucleotides or nucleotide analogs of one or more but less than all base types.

4. The method of claim 1 , wherein (b) is performed in absence of determining a sequence for any of said first plurality of nucleic acid molecules.

5. The method of claim 1 , wherein said first plurality of nucleic acid molecules contains, at incorporation sites, nucleotides complementary to said subset of nucleotides or nucleotide analogs.

6. The method of claim 1 , wherein said first plurality of nucleic acid molecules contains, at incorporation sites, a greater number of nucleotides complementary to said subset of nucleotides or nucleotide analogs from said plurality of nucleotides or nucleotide analogs in (b) relative to nucleotides of all other base types.

7. The method of claim 1 , wherein said first plurality of nucleic acid molecules does not contain, at incorporation sites, nucleotides that are not complementary to said subset of nucleotides or nucleotide analogs.

8. The method of claim 1 , wherein said subset of nucleotides or nucleotide analogs from said plurality of nucleotides or nucleotide analogs in (b) comprises less than 10%, less than 5%, less than 1%, less than 0.1%, or less than 0.01% of said plurality of nucleotides or nucleotide analogs.

9. The method of claim 1 , wherein a nucleic acid molecule of said first plurality of nucleic acid molecules comprises a priming site.

10. The method of claim 1 , wherein said plurality of nucleotides or nucleotide analogs comprises one or more nucleotides or nucleotide analogs selected from the group consisting of deoxynucleotides and dideoxynucleotides.

11. The method of claim 1 , wherein said plurality of nucleotides or nucleotide analogs comprises nucleotides or nucleotide analogs selected from the group consisting of deoxyadenosine triphosphate (dATP), 2′,3′-dideoxyadenosine-5′triphosphate (ddATP), deoxyguanosine triphosphate (dGTP), 2′,3′-dideoxyguanosine-5′-triphosphate (ddGTP), deoxycytidine triphosphate (dCTP), 2′,3′-dideoxycytidine-5′-triphosphate (ddCTP), deoxythymidine triphosphate (dTTP), 2′,3′-dideoxythymidine-5′-triphosphate (ddTTP), deoxyuridine triphosphate (dUTP), 2′,3′-dideoxyuridine-5′-triphosphate (ddUTP), and a variant thereof.

12. The method of claim 1 , wherein said subset of nucleotides or nucleotide analogs from said plurality of nucleotides or nucleotide analogs in (b) includes bases of a different type from said remainder of said plurality of nucleotides or nucleotide analogs.

13. The method of claim 1 , wherein said incorporating said subset of nucleotides or nucleotide analogs into said first plurality of nucleic acid molecules yields said remainder of said plurality of nucleotides or nucleotide analogs having a purity that is increased relative to a purity of said plurality of nucleotides or nucleotide analogs.

14. The method of claim 1 , wherein said support comprises at least one planar surface.

15. The method of claim 1 , wherein said first reaction space and said second reaction space are a same reaction space.

16. The method of claim 1 , wherein said incorporating in (b) yields double stranded nucleic acid molecules from said first plurality of nucleic acid molecules comprising said subset of nucleotides or nucleotide analogs, and wherein, subsequent to (b), said first reaction space is replenished with an additional plurality of nucleic acid molecules, which additional plurality of nucleic acid molecules does not include said subset of nucleotides or nucleotide analogs.

17. The method of claim 16 , wherein said first reaction space is replenished by denaturation of said double stranded nucleic acid molecules and removal of resultant single stranded nucleic acid molecules that are not immobilized to said support.

18. The method of claim 1 , further comprising repeating (a)-(d) with at least one additional plurality of nucleotides or nucleotide analogs.

19. The method of claim 1 , wherein said support is a solid support.