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.
Claims20
A system for processing a plurality of sequence signals, comprising:
- a database that stores said plurality of sequence signals, said plurality of sequence signals generated upon sequencing of a nucleic acid;
- and
- one or more computer processors coupled to said database, wherein said one or more computer processors are individually or collectively programmed to:
- (a) align said plurality of sequence signals to a reference genome in a reference signal database, wherein the reference genome comprises reference signals;
- (b) identify a reference locus comprising a homopolymer sequence based at least on said aligned sequence signals;
- and
- (c) generate a consensus sequence from said plurality of sequence signals aligned to said reference signal, which consensus sequence comprises a homopolymer sequence of N bases, based at least on said identified reference locus, a length of said homopolymer sequence of said reference locus, and said reference signal.
A system for quantifying context dependency of a plurality of sequence signals, comprising:
- a database that stores said plurality of sequence signals;
- and
- one or more computer processors coupled to said database, wherein said one or more computer processors are individually or collectively programmed to:
- (a) align said plurality of sequence signals to a reference genome in a reference signal database, wherein the reference genome comprises reference signals;
- and
- (b) quantify said context dependency in said plurality of sequence read signals aligned to said reference signal, based at least on a known sequence associated with said plurality of sequence signals.
Dependencies are inferred from the claim text.