The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
Open accessAbstract
False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k -mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k -mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .
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Fast and sensitive protein alignment using DIAMOND
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Kraken: ultrafast metagenomic sequence classification using exact alignments
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Self-citationReagent and laboratory contamination can critically impact sequence-based microbiome analyses
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling
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Cited by
Steinegger, M., & Salzberg, S. L. (2020) · Genome Biology · doi:10.1186/s13059-020-02023-1 · Cited by 246
Self-citationTumor microbiome links cellular programs and immunity in pancreatic cancer
Ghaddar, B., Biswas, A., Harris, C., Omary, M. B., Carpizo, D. R., Blaser, M. J., & De, S. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.09.009 · Cited by 181
Nasko, D. J., Koren, S., Phillippy, A. M., & Treangen, T. J. (2018) · Genome Biology · doi:10.1186/s13059-018-1554-6 · Cited by 170
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
“2F) [19].”
BackgroundCorrecting index databases improves metagenomic studies
Méric, G., Wick, R. R., Watts, S. C., Holt, K. E., & Inouye, M. (2019) · doi:10.1101/712166 · Cited by 34
Metadata
- Authors
- Breitwieser, F. P., Baker, D. N., & Salzberg, S. L.
- Venue
- Genome Biology
- Published
- 2018-11-16
- Volume
- 19
- Issue
- 1
- Pages
- 198-198
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2950964375
- Cited by
- 474
- References
- 31
- FWCI
- 10.99
- Type
- journal article
- Language
- en
- Open access
- gold
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