Patent ID: 8370079

Claim:
A method of determining a consensus sequence, comprising: a) providing a plurality of replicate sequence reads; b) aligning the plurality of replicate sequence reads to generate a multiple sequence alignment; c) determining a percent of majority calls for each position in a region of interest in the multiple sequence alignment; d) based upon the results of step c, identifying a set of sequential positions in the region of interest, wherein all positions in the set of sequential positions have a percent of majority calls below a threshold; and e) using information from the plurality of replicate sequence reads for the set of sequential positions in the region of interest in a pattern classification algorithm to generate a consensus sequence spanning the set of sequential positions, wherein a call by the pattern classification algorithm for a first position in the set of sequential positions is dependent upon a call made for a second position in the set of sequential positions that is made by the pattern classification algorithm, the first position and the second position are adjacent to each other, and at least steps a), b), and e) are performed using a suitably programmed computer.