The loadConstraint command loads a constraint file. The file can be in the NCBI ancillary file format, or in the CAP3 constraint file format. SeqMan NGen uses constraint files to identify paired end reads, similar to using the setPairSpecifier command. Constraint files in the NCBI ancillary file format also contain trimming information, which SeqMan NGen will load and use. SeqMan NGen will create a CAP3 file when saving a Phrap project (.ace) that used paired end constraints.

Parameter Description Allowed values
file The directory and file name of the constraint sequence file. [directory/filename enclosed in quotes]


   file: “/Library/constraints/123_xyz.con”

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