454 Life Sciences Corporation

Chiu Tai Andrew Wong

Yi-Ju Chen

An embodiment of a method for generating a flow order that minimizes the accumulation of phasic synchrony error in sequence data is described that comprises the steps of: (a) generating a plurality of sequential orderings of nucleotides species comprising a k-base length, wherein the sequential orderings define a sequence of introduction of nucleotide species into a sequencing by synthesis reaction environment; (b) simulating acquisition of sequence data from one or more reference genomes using the sequential orderings, wherein the sequence data comprises an accumulation of phasic synchrony error; and (c) selecting one or more of the sequential orderings using a read length parameter and an extension rate parameter.

System and method for generation and use of optimal nucleotide flow orders

Provided herein are methods for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules by detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values.

System and method to correct out of phase errors in DNA sequencing data by use of a recursive algorithm

An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; and revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values.

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Northford, CT, United States of America

Chiu Tai Andrew Wong