BASE-CALLING OF AUTOMATED SEQUENCER TRACES USING PHRED - II - ERROR PROBABILITIES

Elimination of the data processing bottleneck in high-throughput seque ncing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemen ted in our base-calling program phred the ability to estimate a probab ility of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown her e to be valid (correspond to actual error rates] and to have high powe r to discriminate correct base-calls from incorrect ones, For read dat a collected under several different chemistries and electrophoretic co nditions. They play a critical role in our assembly program phrap and our finishing program consed.