The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Sequence-specific error profile of Illumina sequencers
Open accessAbstract
We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers.
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
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
Tablet-next generation sequence assembly visualization.
Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F., & Marshall, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp666 · Cited by 666
Unlocking short read sequencing for metagenomics
Rodrigue, S., Materna, A. C., Timberlake, S. C., Blackburn, M. C., Malmstrom, R. R., Alm, E. J., & Chisholm, S. W. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011840 · Cited by 168
Cited by
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt593 · Cited by 4,497
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma
Schwartzentruber, J., Korshunov, A., Liu, X.-Y., Jones, D. T. W., Pfaff, E., Jacob, K., Sturm, D., Fontebasso, A. M., Quang, D.-A. K., Tönjes, M., et al. (2012) · Nature · doi:10.1038/nature10833 · Cited by 2,631
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
(2015) · doi:10.7717/peerj.1165 · Cited by 1,960
Metadata
- Authors
- Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A., Takahashi, H., Altaf-Ul-Amin, M., Ogasawara, N., & Kanaya, S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-05-14
- Volume
- 39
- Issue
- 13
- Pages
- e90-e90
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2087464200
- Cited by
- 600
- References
- 10
- FWCI
- 22.69
- Type
- journal article
- Language
- en
- Open access
- gold
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: Sequence-specific error profile of Illumina sequencers. https://app.cochat.ai/papers/10.1093/nar/gkr344
- The paper
- Nakamura, K., Oshima, T., Morimoto, T., Ikeda, S., Yoshikawa, H., Shiwa, Y., Ishikawa, S., Linak, M. C., Hirai, A., Takahashi, H., Altaf-Ul-Amin, M., Ogasawara, N., & Kanaya, S. (2011). Sequence-specific error profile of Illumina sequencers. Nucleic Acids Research. https://doi.org/10.1093/nar/gkr344
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.
