The settings in the Trimming section of the Mutation Project Settings, located on the Contig tab, help define the boundaries of the Comparison Region (region used for automatic mutation detection).
Quality Trim is always selected and cannot be deselected. This requires a S/N Ratio of at least 15 for 7 of 9 consecutive bases for Comparison Region inclusion.
Vector Trim enables masking of a vector sequence which could prevent proper alignment. This setting requires loading a SEQ file that has the defined vector sequence.
End Trim settings allow a user-defined number of bps to be ignored at the selected end(s).
Score Trim adds another set of restrictions for the Comparison Region based on phred-like scores. This setting uses a requirement where 7 of 9 consecutive bases must meet the set value in order for that region to be considered within the Comparison Region.
When more than one trim setting is selected, the software will apply the setting that results in the smallest Comparison Region (most number of “trimmed” bases). Quality Trim is then performed after application of the first trim method.