For preprocessing part with host removal: Where do you find the abbreviations for each host species available (e.g. bos is cow, homo is human..)?

The abbreviation (i.e. the genus) is the first word in the list of possible hosts. The names are the scientific names for species, which would be shown on the taxonomy tree if you would look up the common name (i.e. bovine) on Wikipedia.

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{% snippet  topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/faqs/ %}
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Resource purlPURL: