The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
Open accessAbstract
Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. Availability: The software is available at http://icorn.sourceforge.net Contact: tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Cited by
Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031
Self-citationA cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
Sinha, A., Hughes, K. R., Modrzynska, K. K., Otto, T. D., Pfander, C., Dickens, N. J., Religa, A. A., Bushell, E., Graham, A. L., Cameron, R., et al. (2014) · Nature · doi:10.1038/nature12970 · Cited by 438
Self-citationDowning, T., Imamura, H., Decuypere, S., Clark, T. G., Coombs, G. H., Cotton, J. A., Hilley, J. D., de Doncker, S., Maes, I., Mottram, J. C., et al. (2011) · Genome Research · doi:10.1101/gr.123430.111 · Cited by 423
Self-citationEvolutionary analysis of the most polymorphic gene family in falciparum malaria
Otto, T. D., Assefa, S. A., Böhme, U., Sanders, M. J., Kwiatkowski, D. P., Pf3k consortium, Berriman, M., & Newbold, C. (2019) · Wellcome Open Research · doi:10.12688/wellcomeopenres.15590.1 · Cited by 90
Self-citation
Metadata
- Authors
- Otto, T. D., Sanders, M., Berriman, M., & Newbold, C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-06-18
- Volume
- 26
- Issue
- 14
- Pages
- 1704-1707
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2099333915
- Cited by
- 213
- References
- 1
- FWCI
- 4.84
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. https://app.cochat.ai/papers/10.1093/bioinformatics/btq269
- The paper
- Otto, T. D., Sanders, M., Berriman, M., & Newbold, C. (2010). Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics. https://doi.org/10.1093/bioinformatics/btq269
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.
