Hi guys, in Galaxy there is a tool named "krakentool: extract reads by ID" that take in input the classification file from kraken2, the taxa IDs i'm interested in and extract the reads from the classification file with those taxa id. The results between kraken and bracken (at species level) are very different and i want to extract the reads re-assigned from bracken, but bracken doesn't output a classification file but only a report file that i can't use in the krakentool... how can i do?

Thanks for the answers.