Publications

Detailed Information

Metagenome analysis using the Kraken software suite

Cited 83 time in Web of Science Cited 94 time in Scopus
Authors

Lu, Jennifer; Rincon, Natalia; Wood, Derrick E.; Breitwieser, Florian P.; Pockrandt, Christopher; Langmead, Ben; Salzberg, Steven L.; Steinegger, Martin

Issue Date
2022-12
Publisher
Nature Publishing Group
Citation
Nature Protocols, Vol.17 No.12, pp.2815-2839
Abstract
Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment. The authors provide a guide to using the Kraken suite for metagenomics analysis, including classification, quantification and visualization, illustrated by quantification of species in the microbiome and identification of pathogens in a clinical sample.
ISSN
1754-2189
URI
https://hdl.handle.net/10371/202517
DOI
https://doi.org/10.1038/s41596-022-00738-y
Files in This Item:
There are no files associated with this item.
Appears in Collections:

Related Researcher

  • College of Natural Sciences
  • School of Biological Sciences
Research Area Development of algorithms to search, cluster and assemble sequence data, Metagenomic analysis, Pathogen detection in sequencing data

Altmetrics

Item View & Download Count

  • mendeley

Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.

Share