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 be...

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Detalles Bibliográficos
Autores principales: Wood, Derrick E., Lu, Jennifer, Langmead, Ben
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883579/
https://www.ncbi.nlm.nih.gov/pubmed/31779668
http://dx.doi.org/10.1186/s13059-019-1891-0
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author Wood, Derrick E.
Lu, Jennifer
Langmead, Ben
author_facet Wood, Derrick E.
Lu, Jennifer
Langmead, Ben
author_sort Wood, Derrick E.
collection PubMed
description 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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spelling pubmed-68835792019-12-03 Improved metagenomic analysis with Kraken 2 Wood, Derrick E. Lu, Jennifer Langmead, Ben Genome Biol Short Report 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. BioMed Central 2019-11-28 /pmc/articles/PMC6883579/ /pubmed/31779668 http://dx.doi.org/10.1186/s13059-019-1891-0 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Short Report
Wood, Derrick E.
Lu, Jennifer
Langmead, Ben
Improved metagenomic analysis with Kraken 2
title Improved metagenomic analysis with Kraken 2
title_full Improved metagenomic analysis with Kraken 2
title_fullStr Improved metagenomic analysis with Kraken 2
title_full_unstemmed Improved metagenomic analysis with Kraken 2
title_short Improved metagenomic analysis with Kraken 2
title_sort improved metagenomic analysis with kraken 2
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883579/
https://www.ncbi.nlm.nih.gov/pubmed/31779668
http://dx.doi.org/10.1186/s13059-019-1891-0
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