Base-calling of automated sequencer traces using phred. I. Accuracy Assessment-英文文献.pdf

RESEARCH Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Brent Ewing,1 LaDeana Hillier,2 Michael C. Wendl,2 and Phil Green1,3 1Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730 USA; 2Genome Sequencing Center, Washington University School of Medicine, Saint Louis, Missouri 63108 USA The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-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. Progress in this respect will require both improved accuracy of the data processing software and reliable accuracy measures to reduce the need for human involvement in error correction and make human review more efficient. Here, we describe one step toward that goal: a base-calling program for automated sequencer traces, phred, with improved accuracy. phred appears to be the first base-calling program to achieve a lower error rate than the ABI software, averaging 40%–50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry. Overview of Sequence Data Processing lane (in the case of dye–terminator chemistry, this also allows all four reactions to be carried out in a At present, nearly all DNA sequencing is done using