Improved metagenomic analysis with Kraken 2

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 b...

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Vydáno v:Genome Biology Ročník 20; číslo 1; s. 257
Hlavní autoři: Wood, Derrick E., Lu, Jennifer, Langmead, Ben
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 28.11.2019
Springer Nature B.V
BMC
Témata:
Algorithms
Alignment-free methods
Animal Genetics and Genomics
Bioinformatics
Biomedical and Life Sciences
data analysis
Evolutionary Biology
Human Genetics
Life Sciences
Metagenomics
Metagenomics - methods
Metagenomics classification
Microbial Genetics and Genomics
Microbiome
Minimizers
Plant Genetics and Genomics
Probabilistic data structures
Short Report
Software
Taxonomy
translation (genetics)
Metagenomics classification
Metagenomics
Probabilistic data structures
Alignment-free methods
Minimizers
Microbiome
ISSN:1474-760X, 1474-7596, 1474-760X
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Shrnutí: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1891-0