Occasionally contigs require more drastic changes than simple basecall edits. Sometimes it is necessary to remove readings that have been put in the wrong place, or to break contigs that should not have been joined. Gap4 contains functions to help with these problems, and two types of interface.
If a contig needs to be broken cleanly into two new contigs, with all the readings, other than the two at the incorrect join, still linked together, then Break Contig (see section Breaking Contigs), or (see section Break Contig) should be used. The former interface is available via the main gap4 Edit menu, and the latter as an option in the Contig Editor.
If one or more readings need removing from from contig(s), even if their removal will break the contiguity of a contig, then (see section Disassemble Readings), or (see section Remove Reading) should be used. The former interface is available via the main gap4 Edit menu, and the latter as an option in the Contig Editor. Readings can be removed from the database completely, or moved to start individual new contigs, one for each reading.