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RESEARCH: Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment
- Brent Ewing,
- LaDeana Hillier,
- Michael C. Wendl,
- and Phil Green
Genome Res. March 1, 1998 8: 175-185; doi:10.1101/gr.8.3.175
...sequencing instruments. DNA Sequence 3: 107–110. Ewing, B. and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. (this issue). Giddings, M.C., R.L. Brumley Jr., M. Haker, and L.M. Smith. 1993. An adaptive, object oriented strategy for base-calling...
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Resource: BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing
- Wei-Chun Kao,
- Kristian Stevens,
- and Yun S. Song
Genome Res. October 2009 19: 1884-1895; Published in Advance August 6, 2009, doi:10.1101/gr.095299.109
...it is commonly referred to as the phred quality score. Base-specific quality scores in Bustard By definition, the error probability PðBt 6¼bÞ of a base-call is the sumof the probabilities of the three alternate bases being correct, i.e., PðBt 6¼AÞ = PðBt = CÞ +PðBt = GÞ+PðBt = TÞ; and so on. If we wish...
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Resource: ECHO: A reference-free short-read error correction algorithm
- Wei-Chun Kao,
- Andrew H. Chan,
- and Yun S. Song
Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
...of quality score is that used in phred (Ewing and Green 1998); it is a transformed error probability of a base, defined more precisely as follows: Let er,m denote the probability that rm, themth base of read r, is erroneously called. Then, the phred quality score qr,m for rm is given by qr;m = 10 log10 er...
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METHODS: Automated Finishing with Autofinish
- David Gordon,
- Cindy Desmarais,
- and Phil Green
Genome Res. April 1, 2001 11: 614-625; doi:10.1101/gr.171401
...final error rate as the human finisher. For the four projects combined, we estimate an additional 64 reads would have been required, for a total of 608 reads, about 12% more than in the Human-only projects. Because of improvements in Autofinish and Phred ( Ewing et al. 1998 ) since this competition, we...
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Resource: Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
- Wei Qu,
- Shin-ichi Hashimoto,
- and Shinichi Morishita
Genome Res. July 2009 19: 1309-1315; Published in Advance May 13, 2009, doi:10.1101/gr.089151.108
...Bastide M, McCombie WR, Hannon GJ. 2008. AltaCyclic: A self-optimizing base caller for next-generation sequencing.Nat Methods 5: 679–682. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186–194. Hashimoto S, Suzuki Y, Kasai Y, Morohoshi...
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Methods: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
- Bastien Chevreux,
- Thomas Pfisterer,
- Bernd Drescher,
- Albert J. Driesel,
- Werner E.G. Müller,
- Thomas Wetter,
- and Sándor Suhai
Genome Res. June 2004 14: 1147-1159; Published in Advance May 12, 2004, doi:10.1101/gr.1917404
...detection algorithms use a combination of base-calling error probabilities, trace file analysis, template information, and redundancy analysis. The result is a number of—sometimes partial—real mRNA transcripts, which were present in the clone libraries and consecutively sequenced. It is important to note...
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GENOME METHODS: Automated Sequence Preprocessing in a Large-Scale Sequencing Environment
- Michael C. Wendl,
- Simon Dear,
- Dave Hodgson,
- and LaDeana Hillier
Genome Res. September 1, 1998 8: 975-984; doi:10.1101/gr.8.9.975
.... Error probabilities. Genome Res. 8 : 186 – 194 . ↵ Ewing B.G. , Hillier L. , Wendl M.C. , Green P. ( 1998 ) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 : 175 – 185 . ↵ Gleeson T. , Hillier L. ( 1991 ) A trace display and editing program for data from...
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Methods: Inference of population genetic parameters in metagenomics: A clean look at messy data
- Philip L.F. Johnson and
- Montgomery Slatkin
Genome Res. October 2006 16: 1320-1327; Published in Advance September 5, 2006, doi:10.1101/gr.5431206
...of automated sequencer traces using phred. II. Error probabilities . Genome Res. 8 : 186 – 194 . ↵ Ewing, B. , Hillier, L. , Wendl, M.C. , Green, P. ( 1998 ) Base-calling of automated sequencer traces using phred . I. Accuracy assessment. Genome Res. 8 : 175 – 185 . ↵ Feil, E.J. , Spratt, B.G. ( 2001...
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Methods: Systematic Recovery and Analysis of Full-ORF Human cDNA Clones
- Ágnes Baross,
- Yaron S.N. Butterfield,
- Shaun M. Coughlin,
- Thomas Zeng,
- Malachi Griffith,
- Obi L. Griffith,
- Anca S. Petrescu,
- Duane E. Smailus,
- Jaswinder Khattra,
- Helen L. McDonald,
- Sheldon J. McKay,
- Michelle Moksa,
- Robert A. Holt,
- and Marco A. Marra
Genome Res. October 15, 2004 14: 2083-2092; doi:10.1101/gr.2473704
...., Fockler, C., Barnes, W.M., and Higuchi, R. 1994 . Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl. Acad. Sci. 91 : 5695 -5699. ↵ Ewing, B. and Green, P. 1998 . Base-calling of automated sequencer traces using Phred . II. Error probabilities. Genome Res. 8...
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METHODS: Basecalling with LifeTrace
- Dirk Walther,
- Gábor Bartha,
- and Macdonald Morris
Genome Res. May 1, 2001 11: 875-888; doi:10.1101/gr.177901
...sequence, Method 1 will tend to gather error statistics for regions where both basecallers generate few errors. It is possible, however, that what is given as additionally aligned bases in Method 1 for LifeTrace are in fact high-confidence base calls with few errors for a region where Phred introduces...

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