The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing
Open accessAbstract
PCR amplicon deep sequencing continues to transform the investigation of genetic diversity in viral, bacterial, and eukaryotic populations. In eukaryotic populations such as Plasmodium falciparum infections, it is important to discriminate sequences differing by a single nucleotide polymorphism. In bacterial populations, single-base resolution can provide improved resolution towards species and strains. Here, we introduce the SeekDeep suite built around the qluster algorithm, which is capable of accurately building de novo clusters representing true, biological local haplotypes differing by just a single base. It outperforms current software, particularly at low frequencies and at low input read depths, whether resolving single-base differences or traditional OTUs. SeekDeep is open source and works with all major sequencing technologies, making it broadly useful in a wide variety of applications of amplicon deep sequencing to extract accurate and maximal biologic information.
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Cites
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698
FLASH: fast length adjustment of short reads to improve genome assemblies
Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366
Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer
Dawson, S.-J., Tsui, D. W. Y., Murtaza, M., Biggs, H., Rueda, O. M., Chin, S.-F., Dunning, M. J., Gale, D., Forshew, T., Mahler-Araujo, B., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1213261 · Cited by 2,207
Cited by
Karst, S. M., Ziels, R. M., Kirkegaard, R. H., Sørensen, E. A., McDonald, D., Zhu, Q., Knight, R., & Albertsen, M. (2021) · Nature Methods · doi:10.1038/s41592-020-01041-y · Cited by 423
Pauvert, C., Buée, M., Laval, V., Edel-Hermann, V., Fauchery, L., Gautier, A., Lesur, I., Vallance, J., & Vacher, C. (2019) · Fungal Ecology · doi:10.1016/j.funeco.2019.03.005 · Cited by 253
CHOIR improves significance-based detection of cell types and states from single-cell data
Sant, C., Mucke, L., & Corces, M. R. (2025) · Nature Genetics · doi:10.1038/s41588-025-02148-8 · Cited by 18
Zhou, G., Hemming-Schroeder, E., Jeang, B., Wang, X., Zhong, D., Lee, M.-C., Li, Y., Bradley, L., Gobran, S. R., David, R. E., et al. (2022) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiac361 · Cited by 11
Metadata
- Authors
- Hathaway, N. J., Parobek, C. M., Juliano, J. J., & Bailey, J. A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-11-30
- Volume
- 46
- Issue
- 4
- Pages
- e21-e21
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2775244680
- Cited by
- 164
- References
- 3
- FWCI
- 4.46
- Type
- journal article
- Language
- en
- Open access
- gold
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- Hathaway, N. J., Parobek, C. M., Juliano, J. J., & Bailey, J. A. (2018). SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1201
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