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Checking Assemblies and Removing Readings

After assembly, and prior to editing, it can be useful to examine the quality of the alignments between individual readings and the sections of the consensus which they overlap. This may reveal doubtful joins between sections of contigs, poorly aligned readings, or readings that have been misplaced. By using this analysis in combination with other gap4 functions such as Find internal joins (see section Find Internal Joins) and Find repeats (see section Find Repeats), it is also possible to discover if readings have been positioned in the wrong copies of repeat elements. The functions for checking the alignment of readings in contigs are described below.See section Checking Assemblies.

If readings are found to be misplaced or need removing for other reasons, gap4 has functions for breaking contigs (see section Breaking Contigs), and removing readings (see section Disassembling Readings). These functions can be accessed through the main gap4 Edit menu or from within the Contig Editor.

If readings are removed from contigs to start new contigs of one reading, these contigs can then be processed by Find internal joins (see section Find Internal Joins) and the Join editor (see section The Join Editor), which should reveal all the other positions at which the reading matches.

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