The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Swarm: robust and fast clustering method for amplicon-based studies
Open accessAbstract
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
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Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
ggplot2: Elegant Graphics for Data Analysis
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Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
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PANDAseq: paired-end assembler for Illumina sequences
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G., & Neufeld, J. D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-31 · Cited by 2,132
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
Cited by
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Krause, S., Molari, M., Gorb, E. V., Gorb, S. N., Kossel, E., & Haeckel, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-66361-7 · Cited by 125
Shift in skin microbiota of Western European women across aging
Jugé, R., Rouaud-Tinguely, P., Breugnot, J., Servaes, K., Grimaldi, C., Roth, M.-P., Coppin, H., & Closs, B. (2018) · Journal of Applied Microbiology · doi:10.1111/jam.13929 · Cited by 112
Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Hansen, M. E. B., Rubel, M. A., Bailey, A. G., Ranciaro, A., Thompson, S. R., Campbell, M. C., Beggs, W., Dave, J. R., Mokone, G. G., Mpoloka, S. W., et al. (2019) · Genome Biology · doi:10.1186/s13059-018-1616-9 · Cited by 110
A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Sternes, P. R., Lee, D., Kutyna, D. R., & Borneman, A. R. (2017) · GigaScience · doi:10.1093/gigascience/gix040 · Cited by 91
Metadata
- Authors
- Mahé, F., Rognes, T., Quince, C., de Vargas, C., & Dunthorn, M.
- Venue
- PeerJ
- Publisher
- PeerJ
- Published
- 2014-09-25
- Volume
- 2
- Pages
- e593
- ISSN
- 2167-8359 (ISSN-L)
- OpenAlex
- W2160209604
- Cited by
- 978
- References
- 7
- FWCI
- 19.10
- Type
- journal article
- Language
- en
- Open access
- gold
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- Mahé, F., Rognes, T., Quince, C., de Vargas, C., & Dunthorn, M. (2014). Swarm: robust and fast clustering method for amplicon-based studies. PeerJ. https://doi.org/10.7717/peerj.593
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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.
