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

Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Shavlik, and Frederick R. Blattner

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.

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