Base-Calling of Automated Sequencer Traces UsingPhred.II. Error Probabilities

Base-calling of automated sequencer traces using phred. II. Error probabilities.

Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error prob...

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

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, impro...

Dna Sequences Base Calling by Phred: Error Pattern Analysis

PHRED is the most frequently used base caller algorithm in genome projects. An interesting point on PHRED utilization is the fact that a low score on some base may not actually correspond to a miscalling on that base, but it may stand for a putative error on the region around this base. In order to evaluate the efficiency of PHRED on base calling and base quality assigning, we have sequenced pU...

An Intelligent System for Automated DNA Base Calling

Dynamic range of fluorescence detection and base-calling accuracy in DNA sequencer based on single-photon counting.

Recently, we developed a family of high-performance automated capillary DNA sequencing instruments based on a single-photon detection of fluorescently labeled DNA fragments. Our machines employ digital and broadband techniques, essential for achieving superior instrument sensitivity and dynamic range. In the present paper, we discuss limitations of the instrument's performance caused by the non...