Increasing Consensus Accuracy in DNA Fragment Assemblies by Incorporating Fluorescent Trace Representations

We present a new method for determining the consensus sequence in DNA fragment assemblies. The new method, Trace-Evidence, directly incorporates aligned ABI trace information into consensus calculations via our previously described representation, Trace-Data Classifications. The new method extracts and sums evidence indicated by the representation to determine consensus calls. Using the Trace-Evidence method results in automatically produced consensus sequences that are more accurate and less ambiguous than those produced with standard majority-voting methods. Additionally, these improvements are achieved with less coverage than required by the standard methods-using Trace-Evidence and a coverage of only three, error rates are as low as those with a coverage of over ten sequences.