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.

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.

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)