US 11,655,500 B2
Methods, systems, and computer readable media for repeat sequencing
Earl Hubbell, Palo Alto, CA (US); Christian Koller, San Francisco, CA (US); and Nils Homer, Arlington, MA (US)
Assigned to Life Technologies Corporation, Carlsbad, CA (US)
Filed by LIFE TECHNOLOGIES CORPORATION, Carlsbad, CA (US)
Filed on Jun. 3, 2019, as Appl. No. 16/429,266.
Application 16/429,266 is a continuation of application No. 14/048,843, filed on Oct. 8, 2013, granted, now 10,329,608.
Claims priority of provisional application 61/712,686, filed on Oct. 11, 2012.
Claims priority of provisional application 61/712,206, filed on Oct. 10, 2012.
Prior Publication US 2020/0024656 A1, Jan. 23, 2020
Int. Cl. C12Q 1/6869 (2018.01); G16B 30/00 (2019.01)
CPC C12Q 1/6869 (2013.01) [G16B 30/00 (2019.02); C12Q 2535/122 (2013.01)] 19 Claims
 
1. A method for sequencing a nucleic acid template, comprising:
(a) performing a first sequencing process on the nucleic acid template to obtain a first sequencing result, wherein the first sequencing process includes flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents;
(b) after the first sequencing process, performing a second sequencing process on the nucleic acid template to obtain a second sequencing result, wherein the second sequencing process includes flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents, wherein the second predetermined ordering of nucleotides and/or reagents is different from the first predetermined ordering of nucleotides and/or reagents and wherein at least one of the first and second predetermined orderings of nucleotides and/or reagents is designed for repeat sequencing; and
(c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result, wherein determining the sequence of bases comprises:
generating sets of candidate sequences of bases for each of first sequencing result and the second sequencing result using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and
selecting from the generated sequences of bases the candidate sequence leading to a highest score or a lowest penalty as corresponding to a correct sequence for the nucleic acid template.