Why there are species call differences between the AMR and mNGS pipelines?

You may want to compare species detected with the AMR and mNGS pipelines. However, it is likely that there will be differences between species detected using these pipelines. Although the AMR and mNGS pipelines use the same assembly workflow and parameters, the species-detection methods are different. Species detected with the AMR module are based on a k-mer classifier that is limited to pathogens and pathogen-associated plasmids found within the Comprehensive Antibiotic Resistance Database (CARD). On the other hand, species detected through the mNGS pipeline are compared to a broader database (GenBank) using DIAMOND and Minimap2. These methodological and reference database discrepancies will lead to differences in species detection between the two pipelines.