Filter Kraken2 output?

Question

[damien_cabral]

Hello,

I am using Kraken2 to perform taxonomic classification on murine gut microbiome samples. This pipeline is detecting a significant number of reads (5-15%) from a bacterial species that I know is a contaminant and I would like to exclude them from downstream analyses. I have used several tools to filter out these contaminating reads before classification (bbduk, kneaddata, etc) but every tool I've tried still leaves several thousands reads that are mapped to my contaminant. Is there any way to filter the Kraken2 output to remove the reads mapping to a specific taxa? Thanks for any help!

[Istvan Albert]

Why is it a problem if those reads are left there? As long as you know these are contaminants you can just as well ignore those results.