Fig. 4

Annotation pipelines. a Identification of ARGs: input nanopore reads are aligned to the DeepARG database using DIAMOND. Alignments are clustered based on their location and annotations are performed using the DeepARG-LS model. b Local Best Hit Approach: identification of the functional genes within the nanopore reads. Alignments are clustered based on their location and the best hit for each cluster is selected. Resulting alignments are filtered out based on sequence alignment quality