Metagenome analysis using the Kraken software suite

Here 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.

Workflows

We provide two jupyter notebooks, each desribing one workflow. Jupyter notebooks can be executed for free using Google Colaboratory, which over cloud compute to execute notebooks.

1. Kraken_microbiom.ipynb describes the microbiom analysis workflow. Open in Colab.
2. Kraken_pathogen.ipynb describes the pathogen detection workflow. Open in Colab.

Publication

Lu J, Rincon N, Wood D E, Breitwieser F P, Pockrandt C, Langmead B, Salzberg S L, Steinegger M. Metagenome analysis using the Kraken software suite. Nature Protocols, doi: 10.1038/s41596-022-00738-y (2022)