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

By Brent Ewing, Philip Green. 1998

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 probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing program consed.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

A review on SNP and other types of molecular markers and their use in animal genetics (2002, methodology): “This last in silico step of identifying the SNPs in the sequence traces, whatever the way they were produced, has greatly beneted from the development of programs estimating the quality of base calling, such as PHRED [ 22 ,23] and of other programs using this quality assessment for polymorphism dete”
Ironing out the wrinkles in the rare biosphere through improved OTU clustering (2010, methodology): “…V6 hypervariable region amplicon libraries produced by the Roche Genome Sequencer 20 System (GS 20) have a per-base error rate of 0.25% (Huse et al., 2007), which is comparable to a average phred score better than 25 on contemporary capillary instruments (Ewing and Green, 1998; Ewing et al., 1998).”
A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, methodology): “CAP3 [46] or Phrap [ 45 ] can cluster, assemble and generate consensus contigs from preprocessed EST fragments and ESTscan2 [62] will then detect coding regions in consensus contigs.”
DNA sequence quality trimming and vector removal (2001, methodology): “Thanks to a few powerful chromatogram base-calling programs like phred (Ewing et al., 1998; Ewing and Green, 1998) and TraceTuner (Paracel, 2000), the quality value for each individual base of a raw sequence can be estimated.”
Fertility restorer locus Rf1 of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12 (2005, methodology): “Base calling and quality assessment was conducted with the PHRED program (Ewing and Green 1998; Ewing et al. 1998).”
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments (2010, methodology): “quality scores for the other seven lanes [[15], Supplementary Information, p. 7]. Bustard can also be run using the auto-calibration method, which scores basecalls in a manner similar to the phred base-caller [ 17 ] and does not require a control lane per flow-cell.”
An SNP map of the human genome generated by reduced representation shotgun sequencing (2000, background): “Computer programs that estimate sequence accuracy (such as PHRE”
Efficient storage of high throughput DNA sequencing data using reference-based compression. (2011, methodology): “Much of the efficiency of our method relies on appropriate use of Golomb codes (Golomb 1966) that are now a standard compression technique for storing integer values.”
Using quality scores and longer reads improves accuracy of Solexa read mapping (2008, background): “Sequencing quality scores, introduced in the Phred algorithm [6, 7], assign a probability to the four possible nucleotides for each sequenced base.”
Genome assembly reborn: recent computational challenges (2009, background): “All current sequencing technologies produce an estimate of the quality of the data being produced, in the form of phred quality values [18, 19]—the logarithm of the probability that a particular base in the sequence was incorrectly read.”