Figure 2. Generalized flowchart of vAMPirus v2.1.0, illustrating its configuration (box A), default analyses and programs used within the read processing (box B) and Analyze (boxes C and D) pipelines. For simplicity, only selected connections between processes are highlighted; processes generating the unique amino acid sequences (‘aminotypes’) and clustered ASVs (‘cASVs’), as well as those specific to the DataCheck pipeline (see Supplemental Figure S2) are omitted. See Supplemental Figures S1, S2, and S3 for a more comprehensive illustration of vAMPirus pipelines and the processes therein.