Correction to: Nature Protocols https://doi.org/10.1038/s41596-022-00738-y, published online 28 September 2022.

In the version of the article initially published, in Procedure 1, Step 2, the text “When running paired sequencing reads, use the --paired option for Kraken2 to match read mates and classify the combined mates together” was missing. Additionally, in the same step, three instances of “--paired” have now been added to the code. These corrections have been made to the HTML and PDF versions of the article.