From Array Suite Wiki
When set to true, AutoPenalty will use the following calculation to set the penalty for alignment:
By default, OSA determines the maximal penalty of an alignment. The maximal penalty is defined as the maximal number of mismatches allowed plus the gap penalty if an indel is present in the alignment. Usually we set the gap penalty to one or two (default is two). By default, Omicsoft automatically set the maximal penalty for each read to Max (2, (read length - 31) / 15) based on trimmed read length. Below is a table of automatic penalty for reads with 17- 106 nt.
The oshell default value=True.
When AutoPenalty=True, fixed penalty is not used.
For more information on penalties, see Alignment Penalty.