Flag	Description	Default
-f	Indicates input file is fasta format	Fastq file format
-a	Uses alternative hashing algorithm for calculation74	Ratcliff-Obershelp based algorithm73
-o	Output file with calculated indel rates and statistics	calc_indel_out.csv
-i	Input file with sample name, fasta or fastq file name, guide sequence, PCR target amplicon, and experimental or control in columns from left to right	sample_sheet.csv
-v or -q	Increase or decrease reporting as script runs	Standard reporting
-no-m	Does not perform MLE correction	MLE correction is performed