Improved metagenomic analysis with Kraken 2
Top Cited Papers
Open Access
- 28 November 2019
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 20 (1), 1-13
- https://doi.org/10.1186/s13059-019-1891-0
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.Funding Information
- Directorate for Computer and Information Science and Engineering (IIS-1349906)
- National Institute of General Medical Sciences (R01-GM118568, R35-GM130151)
This publication has 35 references indexed in Scilit:
- Extending reference assembly modelsGenome Biology, 2015
- Kraken: ultrafast metagenomic sequence classification using exact alignmentsGenome Biology, 2014
- Metagenomic microbial community profiling using unique clade-specific marker genesNature Methods, 2012
- The NCBI Taxonomy databaseNucleic Acids Research, 2011
- The sequence read archive: explosive growth of sequencing dataNucleic Acids Research, 2011
- A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA SequencesJournal of Computational Biology, 2006
- Reducing storage requirements for biological sequence comparisonBioinformatics, 2004
- Imbroglios of Viral Taxonomy: Genetic Exchange and Failings of Phenetic ApproachesJournal of Bacteriology, 2002
- [33] Analysis of compositionally biased regions in sequence databasesMethods in Enzymology, 1996
- Probabilistic counting algorithms for data base applicationsJournal of Computer and System Sciences, 1985