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Bowtie2 mode for Host decontamination of metagenomic samples using proxy species

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  • Bowtie2 mode for Host decontamination of metagenomic samples using proxy species

    Hi,
    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.

    Kraken2 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.

    The traditional approach to preprocessing is to map reads to host genomes in order to decontaminate the samples in silico, using BWT aligners such as Bowtie2 in our case.

    Here are my two questions/topics of discussion :

    1. We want to use P. patens' genome to decontaminate the sample; do any arguments against that come to mind?
    2. We wonder which Bowtie2 mode — local or end-to-end — to use when doing so, and why.

    Looking forward to read you thoughts on the matter.
    Cheers!
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