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Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment
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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, improved automation will be essential, and it is particularly important that human involvement in sequence data processing be significantly reduced or eliminated. Progress in this respect will require both improved accuracy of the data processing software and reliable accuracy measures to reduce the need for human involvement in error correction and make human review more efficient. Here, we describe one step toward that goal: a base-calling program for automated sequencer traces,phred,with improved accuracy.phred appears to be the first base-calling program to achieve a lower error rate than the ABI software, averaging 40%–50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
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“Additional Sanger sequencing was performed to improve the assembly quality of the isoform terminal regions and was integrated using Phred 54 and CAP3 (ref.”
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A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions
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Comparative studies of de novo assembly tools for next-generation sequencing technologies
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Genomics of an extreme psychrophile, Psychromonas ingrahamii
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Cryptococcus neoformans Gene Expression during Experimental Cryptococcal Meningitis
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Deep learning in biomedical data science
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Iron in micronutrient Powder promotes an Unfavorable gut microbiota in Kenyan infants
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“The sorted paired reads were assembled using phrap [19,20].”
Method
Metadata
- Authors
- Ewing, B., Hillier, L., Wendl, M. C., & Green, P.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1998-03-01
- Volume
- 8
- Issue
- 3
- Pages
- 175-185
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2121016876
- Cited by
- 6,967
- References
- 2
- Type
- posted content
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
