The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Open accessAbstract
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.
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“yields an inferred sequence accuracy in the assembly of not less than 99.99910%, corresponding to a Phred score54 of no less than 50.4839 in these coding regions.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [54]
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Cites
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint
Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993
Self-citationConsed: a graphical tool for sequence finishing.Preprint
Gordon, D., Abajian, C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.195 · Cited by 3,706
Self-citationLee, L. G., Connell, C. R., Woo, S. L., Cheng, R. D., McArdle, B. F., Fuller, C. W., Halloran, N. D., & Wilson, R. K. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.10.2471 · Cited by 170
AmpliTaq ® DNA Polymerase, FS Dye-Terminator Sequencing: Analysis of Peak Height Patterns
Parker, L., Zakeri, H., Deng, Q., Spurgeon, S. L., Kwok, P., & Nickerson, D. A. (1996) · BioTechniques · doi:10.2144/96214rr02 · Cited by 83
An adaptive, object oriented strategy for base calling in DNA sequence analysis
Giddings, M. C., Brumley, R. L., Haker, M., & Smith, L. M. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.19.4530 · Cited by 51
Assignment of position-specific error probability to primary DNA sequence data
Lawrence, C. B., & Solovyev, V. V. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.7.1272 · Cited by 40
A graph theoretic approach to the analysis of DNA sequencing data.Preprint
Berno, A. J. (1996) · Genome Research · doi:10.1101/gr.6.2.80 · Cited by 40
Golden, J. B., Torgersen, D. L., & Tibbetts, C. (1993) · PubMed · Cited by 27
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,260
Metadata
- Authors
- Ewing, B., & Green, P.
- Affiliations
- University of Washington (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1998-03-01
- Volume
- 8
- Issue
- 3
- Pages
- 186-194
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2119923823
- Cited by
- 5,439
- References
- 8
- Citations by year
- 2026: 56 · 2025: 88 · 2024: 84 · 2023: 86 · 2022: 115 · 2021: 157 · 2020: 141 · 2019: 128 · 2018: 132 · 2017: 176 · 2016: 190 · 2015: 215 · 2014: 275 · 2013: 301 · 2012: 289
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
- Keywords
- base calling, error probability estimation, next-generation sequencing, sequencing accuracy, genome assembly
- MeSH terms
- Base Sequence, Chimera, Cloning, Molecular, Data Interpretation, Statistical, Genetic Vectors, Humans, Probability, Quality Control, Software, Reproducibility of Results, Discriminant Analysis, Human Genome Project, Sequence Analysis, DNA
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