TABLE 1.

Selected criteria being input from the users.

Option	Type	Details
pairedData	T or F	Boolean variable that indicates whether data are paired T or single F
UMIlocation	R1 or R1 and R2	Variable that indicates whether UMI is located only in R1 or R1 and R2
UMIlength	Numeric	The length of the UMI sequence
sequenceLength	Numeric	The length of the read sequence
countsCutoff	Numeric	Min read counts per UMI, for initial data cleaning
UMIdistance	Numeric	Max UMI distance for UMI merging
sequenceDistance	Numeric	Max sequence distance for UMI merging with the associated reads