The DOI matches its Crossref record; 28 of the 28 references it cites were found in a registry or an index.
Fast and sensitive taxonomic classification for metagenomics with Kaiju
Open accessAbstract
Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k -mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k -mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk .
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Pérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314
Lindefeldt, M., Eng, A., Darban, H., Bjerkner, A., Zetterström, C. K., Allander, T., Andersson, B., Borenstein, E., Dahlin, M., & Prast-Nielsen, S. (2019) · npj Biofilms and Microbiomes · doi:10.1038/s41522-018-0073-2 · Cited by 310
Leech, J., Cabrera-Rubio, R., Walsh, A. M., Macori, G., Walsh, C. J., Barton, W., Finnegan, L., Crispie, F., O’Sullivan, O., Claesson, M. J., et al. (2020) · mSystems · doi:10.1128/msystems.00522-20 · Cited by 200
Metadata
- Authors
- Menzel, P., Ng, K. L., & Krogh, A.
- Venue
- Nature Communications
- Published
- 2016-04-13
- Volume
- 7
- Issue
- 1
- Pages
- 11257-11257
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2337747100
- Cited by
- 2,118
- References
- 28
- FWCI
- 40.33
- Type
- journal article
- Language
- en
- Open access
- gold
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