Methods and systems for sequence calling
AssigneeUltima Genomics, Inc.
InventorsMark Pratt, Gilad Almogy, Avishai Bartov
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Abstract
The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.
Claims24
A method for generating a consensus sequence, comprising:
- (a) sequencing a nucleic acid to provide a plurality of sequence signals and a plurality of imputed sequences, wherein said plurality of imputed sequences comprises a plurality of homopolymer sequences;
- (b) truncating said plurality of homopolymer sequences to provide a plurality of HpN truncated sequences comprising truncated homopolymer sequences of N bases in length;
- (c) aligning said plurality of HpN truncated sequences to a truncated reference sequence, wherein said truncated reference sequence comprises a truncated reference genome comprising one or more reference homopolymer sequences of N bases in length;
- and
- (d) generating said consensus sequence based at least in part on said aligning in (c), wherein said consensus sequence comprises one or more consensus homopolymer sequences of N bases in length and wherein generating said consensus sequence comprises determining lengths of at least a subset of said plurality of homopolymer sequences based at least in part on clustering of said at least said subset of said plurality of homopolymer sequences or said plurality of sequence signals associated therewith.
A method for quantifying a context dependency of a plurality of sequence signals, the method comprising:
- (a) sequencing a nucleic acid to provide said plurality of sequence signals and a plurality of imputed sequences, wherein said nucleic acid comprises a pre-determined sequence, and wherein said plurality of imputed sequences comprises a plurality of homopolymer sequences;
- (b) truncating said plurality of homopolymer sequences to provide a plurality of HpN truncated sequences comprising truncated homopolymer sequences of N bases in length;
- (c) aligning said plurality of HpN truncated sequences to a truncated reference sequence, wherein said truncated reference sequence comprises a truncated reference genome comprising one or more reference homopolymer sequences of N bases in length;
- and
- (d) quantifying said context dependency of said plurality of sequence signals based at least in part on (i) said pre-determined sequence and (ii) said aligning in (c).
A system for quantifying a context dependency of a plurality of sequence signals, comprising:
- a database for storing said plurality of sequence signals and a plurality of imputed sequences, wherein said plurality of imputed sequences comprises a plurality of homopolymer sequences, and wherein said plurality of sequence signals and said plurality of imputed sequences correspond to a nucleic acid comprising a pre-determined sequence;
- and
- one or more computer processors coupled to said database, wherein said one or more computer processors are individually or collectively programmed to:
- (a) truncate said plurality of homopolymer sequences to provide a plurality of HpN truncated sequences comprising truncated homopolymer sequences of N bases in length;
- (b) align said plurality of HpN truncated sequences to a truncated reference sequence, wherein said truncated reference sequence comprises a truncated reference genome comprising one or more reference homopolymer sequences of N bases in length;
- and
- (c) quantify said context dependency of said plurality of sequence signals based at least in part on (i) said pre-determined sequence and (ii) said aligning in (b).
Dependencies are inferred from the claim text.