The setContaminantParam command allows you to adjust the parameters used for scanning for contaminant sequences. In order to be applied, this command must appear in the script before the loadContaminant command, and the contamScan parameter for the assemble command must be set to true.

Parameter Description Allowed values
MerLength The minimum length of a mer required to be considered an exact match when scanning for contaminants. Wizard equivalent: Advanced Trim/Scan Options > Mer length. [number from 5-50]

Default = 17
MinMerMatch The minimum number of matching mers required to mark the sequence as a contaminant. Wizard equivalent: Advanced Trim/Scan Options > Minimum matches. [number from 1-50]

Default = 12


setContaminantParam MerLength:17
setContaminantParam MinMerMatch:12

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