The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
Benchmarking Metagenomics Tools for Taxonomic Classification
Open accessAbstract
Summary Metagenomic sequencing is revolutionizing the detection and characterization of microbial species, and a wide variety of software tools are available to perform taxonomic classification of this data. The fast pace of development of these tools, alongside the complexity of metagenomic data, make it important that researchers are able to benchmark their performance. Here, we review current approaches for metagenomic analysis and evaluate the performance of 20 metagenomic classifiers using simulated and experimental datasets. We describe the key metrics used to assess performance, offer a framework for the comparison of additional classifiers, and discuss the future of metagenomic data analysis.
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Cites
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Cited by
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303
Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
Identifying biases and their potential solutions in human microbiome studies
Nearing, J. T., Comeau, A. M., & Langille, M. G. I. (2021) · Microbiome · doi:10.1186/s40168-021-01059-0 · Cited by 240
A survey of k-mer methods and applications in bioinformatics
Moeckel, C., Mareboina, M., Konnaris, M. A., Chan, C. S. Y., Mouratidis, I., Montgomery, A., Chantzi, N., Pavlopoulos, G. A., & Georgakopoulos-Soares, I. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.05.025 · Cited by 131
“[257,258] Table 2 ( continued ) Application Description Tools (reference) [272], Taxonomer[273], TETRA[274], VirFinder[18], WGSQuikr[275]”
BackgroundQuantifying bias introduced by sample collection in relative and absolute microbiome measurements
Maghini, D. G., Dvorak, M., Dahlen, A., Roos, M., Doyle, B., Kuersten, S., & Bhatt, A. S. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01754-3 · Cited by 116
Metadata
- Authors
- Ye, S. H., Siddle, K. J., Park, D. J., & Sabeti, P. C.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-08
- Volume
- 178
- Issue
- 4
- Pages
- 779-794
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2968450569
- Cited by
- 593
- References
- 18
- FWCI
- 17.76
- Type
- journal article
- Language
- en
- Open access
- bronze
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