If the reading aligns well with two contigs it is entered into one of them, then the two contigs are compared. If they align well they are joined. If the reading does not match it starts a new contig. If a reading matches but does not align well it can either be entered as a new contig or rejected. A submode allows tagged regions of contigs to be masked and hence restricts the areas into which data is entered.
Users select the types of tags to be used as masks.
If the masking mode is selected the masked regions are not used during the search for exact matches, but they are used during alignment. The effect of this is that new readings that would lie entirely inside masked regions will not produce exact matches and so will not be entered. However readings that have sufficient data outside of masked areas can produce hits and will be correctly aligned even if they overlap the masked data. For this mode the names of readings that do not produce matches are written to the error file with code 5. Note that new readings that carry tags of the types being used for masking will be masked only after they have been entered.