Bowtie2 mode for Host decontamination of metagenomic samples using proxy species

We are profiling the taxonomy of microbial communities on boreal mosses. These mosses’ genome have never been sequenced. We are using Kneaddata for preprocessing and Kraken2 for profiling, which is assigning a significant quantity of reads to Physcomitrium patens, a model organism for mosses. Since the P. patens genome surely has a lot in common with that of other mosses, this makes sense, as host DNA is bound to make its way to the sequencer.

We want to use P. patens’ genome to decontaminate the sample. We wonder which Bowtie2 mode — local or end-to-end — to use when doing so, and if there’s a rationale behind that choice.

Looking forward to read you thoughts on the matter.