Fig. 1: DARTE-QM bioinformatic pipeline.

Boxes colored blue represent reads retained through the pipeline, red were discarded, and green are the finalized reads ready for analysis. Reads were filtered by quality score and demultiplexed by the presence of primer sequences. To classify ARGs, both merged and unmerged reads were required to align to known genes in ResFam and CARD ARG reference databases. In the case of unmerged reads, if both the forward and the reverse read aligned to the same target, the shorter alignment from the pair was discarded.