Table 1.

Flag variables

Flag	Description	Comments
-i	Input directory path and name	Required
-o	Output directory path and name	Optional Default value: /pipeline.output
-p	Extraction forward DNA primer	Optional
-q	Extraction reverse DNA primer	Optional
-T	Number of threads used for computation	Optional Default value: 1
-a	Translation into amino acids is performed	Optional Default value: FALSE
-r	Files for individual lanes are retained	Optional Default value: FALSE
-e	Additional internal PANDAseq flags	Optional Must be entered in quotation marks (e.g., -e “-L 50”) Default value: “-l 1 -d rbfkms“
-h	Help message	Optional