The loadContaminant command loads a contaminant sequence file to be used to identify known contaminants, such as primers, in the assembly. Sequences that contain at least 12 matching 17-mers are flagged as contaminant sequences and will be removed from the assembly.
| Parameter | Description | Allowed values |
|---|---|---|
| file | The directory and file name of the contaminant sequence file. A folder may also be specified, in which case all of the sequence files within that folder will be loaded and used for contaminant screening. | [directory/filename enclosed in quotes] |
Example:
loadContaminant
file: “/Library/contaminants/123_abc.seq”
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