System and method for consensus-calling with per-base quality values for sample assemblies

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The invention relates to a system for basecall resolution comprising at least one module which provides functionality for comparing a plurality of initial basecalls corresponding to one or more overlapping sequence fragments so as to identify agreement between the initial basecalls to generate a consensus basecall; the at least one module further used to perform a re-calling operation when there is a lack of agreement between the initial basecalls using a more rigorous basecalling routine to generate one or more stringent basecalls and thereafter identifying agreement between the initial basecalls and stringent basecalls as the consensus basecall; the at least one module further performing a weighted vote for those basecalls that lack of agreement between the initial basecall and the stringent basecall to identify the consensus basecall as the basecall with the greatest weighted vote and thereafter determining a quality value for the consensus basecall.