Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

@article{citeulike:1314397, abstract = {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.}, address = {Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730, USA.}, author = {Ewing, B. and Hillier, L. and Wendl, M. C. and Green, P. }, citeulike-article-id = {1314397}, doi = {http://dx.doi.org/10.1101/gr.8.3.175}, issn = {1088-9051}, journal = {Genome Res}, month = {March}, number = {3}, pages = {175--185}, posted-at = {2007-05-21 06:32:08}, priority = {2}, title = {Base-calling of automated sequencer traces using phred. I. Accuracy assessment.}, url = {http://dx.doi.org/10.1101/gr.8.3.175}, volume = {8}, year = {1998} }

TY - JOUR ID - citeulike:1314397 L3 - citeulike-article-id:1314397 TI - Base-calling of automated sequencer traces using phred. I. Accuracy assessment. JF - Genome Res VL - 8 IS - 3 SP - 175 EP - 185 AD - Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195-7730, USA. SN - 1088-9051 N2 - 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. AU - Ewing, B AU - Hillier, L AU - Wendl, MC AU - Green, P PY - 1998/03// UR - http://dx.doi.org/10.1101/gr.8.3.175 ER -