The high accuracy of Phred quality scores make them an idealtool to assess the quality of sequences. This highaccuracy has been observed for sequences generated at differentlaboratories, each using a different combination of sequencingenzymes, fluorescent dyes, and gel run conditions ( Richterich1998, Genome Research 8:251-9 ). It has been shown that Phred's error probabilities are veryaccurate - if Phred assigns a quality score of 40 to a base, thechances that this base is called incorrectly are indeed just 1 in10,000 (see Ewinget al.1998b, Genome Research 8:186-94 ). Probability that the base is called wrong The quality scores arelogarithmically linked to error probabilities, as shown in thefollowing table: Quality scores range from 4 to about 60, with higher valuescorresponding to higher quality. After calling bases, Phred examines thepeaks around each base call to assign a quality score to each basecall. Phred's base-specific quality scores are one of the mostinnovative features in Phred. They are also used by PhilGreen's sequence assembly program Phrap to generate betterassemblies how Phred works together with Phrap is described below. Phred quality scores have become widelyaccepted to characterize the quality of sequences, for example tocompare different sequencing methods. Sincethis initial study, ABI has improved their base calling software, and eventuallyincorporated base-specific quality scores similar to Phred scores into their"KB" base caller.Īnother very interesting feature of Phred isthe generation of highly accurate, base-specific quality scores(see next section). One good reason to use Phred for base callingis higher accuracy: in one study, Phred made "40-50%fewer errors" "than the ABI software" ( Ewinget al.1998a, Genome Research 8:175-85 ).
For scientists who would like to use Phred on Windows or Mac OS X from a user-friendly graphical interface, CodonCode Corporation offers CodonCodeAligner. For information about Phrap,Cross_match, and Consed, please visit Since Phred was developed for easy integration into automated data processing pipelines, Phred does not provide a graphical user interface. This page gives a brief description of Phred. Phred iswidely used by the largest academic and commercial DNA sequencinglaboratories.
Phil Green and Brent Ewing, and is distributed by CodonCode Corporation under license from the University of Washington. Phred is a base calling program for DNA sequence traces Phred executables for Windows, Mac OS X, Linux, and Unix are available fromCodonCode Corporation as part of the PHRED - PHRAP package. Phred - Quality Base Calling Phred - Quality Base Calling