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Improved metagenomic analysis with Kraken 2
Open accessPublished version of a preprint
Abstract
Although Kraken’s k -mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.
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Citations
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“As databases of assembled genomes continue to grow, databases of reference sequences used for metagenomics studies will also grow [21,23].”
BackgroundReducing storage requirements for biological sequence comparison
Roberts, M., Hayes, W., Hunt, B. R., Mount, S. M., & Yorke, J. A. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth408 · Cited by 485 · cited 1×
“We also performed a third parameter sweep, focused on translated search (Kraken 2X), where we looked at values for l in the interval [11, 15], values for k in the interval [l, l+3], and values for s in the interval [0, 3].”
Method
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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
Fecal microbiota transplant overcomes resistance to anti–PD-1 therapy in melanoma patients
Davar, D., Dzutsev, A. K., McCulloch, J. A., Rodrigues, R. R., Chauvin, J.-M., Morrison, R. M., Deblasio, R. N., Menna, C., Ding, Q., Pagliano, O., et al. (2021) · Science · doi:10.1126/science.abf3363 · Cited by 1,781
Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01688-w · Cited by 1,442
A unified catalog of 204,938 reference genomes from the human gut microbiome
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Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study.
Ren, L.-L., Wang, Y.-M., Wu, Z.-Q., Xiang, Z.-C., Guo, L., Xu, T., Jiang, Y.-Z., Xiong, Y., Li, Y.-J., Li, X.-W., et al. (2020) · Chinese Medical Journal · doi:10.1097/cm9.0000000000000722 · Cited by 1,349
Metadata
- Authors
- Wood, D. E., Lu, J., & Langmead, B.
- Venue
- Genome Biology
- Published
- 2019-11-28
- Volume
- 20
- Issue
- 1
- Pages
- 257-257
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2990618091
- Cited by
- 7,061
- References
- 7
- FWCI
- 125.68
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/4.0 (tdm)
- creativecommons.org/licenses/by/4.0 (vor)
- Funders
- Directorate for Computer and Information Science and Engineering (IIS-1349906)
- National Institute of General Medical Sciences (R01-GM118568, R35-GM130151)
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