The clc_filter_matches program removes matches of low similarity from a cas file. The limits for low similarity are expressed as a minimum sequence similarity required over a minimum fraction of the read length. These parameters are set using the `-s' and `-l' options, respectively. The limits work just like for clc_ref_assemble_long. For paired reads, if only one read fails to pass the filter criteria, only this one read is removed by default. Use the `-p' option to only include paired reads in the output in such cases.
For further details see Options for All Programs.