BASE-CALLING OF AUTOMATED SEQUENCER TRACES USING PHRED - I - ACCURACYASSESSMENT

The availability of massive amounts of DNA sequence information has be gun to revolutionize the practice of biology. As a result, current lar ge-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obtain the 3-billion-base human genome sequence by the target date of 2005. To reach this goal, improved automation will be essential, and it is particularly important that human involvement in sequence data processing be significantly reduced or eliminated. Progr ess in this respect will require both improved accuracy of the data pr ocessing software and reliable accuracy measures to reduce the need fo r human involvement in error correction and make human review more eff icient. Here, we describe one step toward that goal: a base-calling pr ogram For automated sequencer traces, phred, with improved accuracy. p hred appears to be the first base-calling program to achieve a lower e rror rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running c onditions, or sequencing chemistry.