The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Reply to ‘Errors in long-read assemblies can critically affect protein prediction’
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Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“It is important that more than one round of polishing with Illumina reads are performed on the assemblies, as that reduces any issues that might stem from the long reads (133,134).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [133]
Citations
Cites
Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112963 · Cited by 9,197
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 7,329
Self-citationFast and accurate de novo genome assembly from long uncorrected readsPreprint
Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,094
Phased diploid genome assembly with single-molecule real-time sequencing
Chin, C.-S., Peluso, P., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,904
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Self-citationPerformance comparison of benchtop high-throughput sequencing platforms
Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J., & Pallen, M. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2198 · Cited by 1,337
Self-citationSchneider, V. A., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H.-C., Kitts, P. A., Murphy, T. D., Pruitt, K. D., Thibaud-Nissen, F., Albracht, D., et al. (2017) · Genome Research · doi:10.1101/gr.213611.116 · Cited by 1,193
Self-citationDe novo assembly of haplotype-resolved genomes with trio binning
Koren, S., Rhie, A., Walenz, B. P., Dilthey, A. T., Bickhart, D. M., Kingan, S. B., Hiendleder, S., Williams, J. L., Smith, T. P. L., & Phillippy, A. M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4277 · Cited by 522
Self-citationAssembly and diploid architecture of an individual human genome via single-molecule technologies
Pendleton, M., Sebra, R., Pang, A. W. C., Ummat, A., Franzén, O., Rausch, T., Stütz, A. M., Stedman, W., Anantharaman, T., Hastie, A. R., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3454 · Cited by 474
Long-read sequence assembly of the gorilla genome
Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science · doi:10.1126/science.aae0344 · Cited by 333
Research works printed but not linked: 3
- Koren, S. et al. Preprint at bioRxiv https://doi.org/10.1101/271486 (2018). · DOI
- Lehmann, R. et al. Preprint at bioRxiv https://doi.org/10.1101/278267 (2018). · DOI
- Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. Preprint at https://arxiv.org/abs/1207.3907 (2012). · arXiv
Cited by
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Self-citationTowards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Self-citationTørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Metadata
- Authors
- Koren, S., Phillippy, A. M., Simpson, J. T., Loman, N. J., & Loose, M.
- ORCID
- Loose, Matthew
- Venue
- Nature Biotechnology
- Published
- 2019-01-22
- Volume
- 37
- Issue
- 2
- Pages
- 127-128
- ISSN
- 1087-0156
- 1546-1696
- Cited by
- 30
- References
- 14
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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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.
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Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Reply to ‘Errors in long-read assemblies can critically affect protein prediction’. https://app.cochat.ai/papers/10.1038/s41587-018-0005-y
- The paper
- Koren, S., Phillippy, A. M., Simpson, J. T., Loman, N. J., & Loose, M. (2019). Reply to ‘Errors in long-read assemblies can critically affect protein prediction’. Nature Biotechnology. https://doi.org/10.1038/s41587-018-0005-y
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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.
