10.6 Editing Contigs

Editing a contig is exactly the same as editing an alignment in Geneious Prime. After selecting the contig, click the Allow Editing button in the sequence viewer and you can modify, insert and delete characters like in a standard text editor.

Editing of contigs is done to resolve conflicts between fragments before saving the final consensus. The normal procedure for this is to look through the disagreements in the contig (as described above) and change bases which you believe are bad calls to be the base which you believe is the correct call. This is often decided by looking at the quality for each of the bases and choosing the higher quality one. Geneious can do this automatically for you if you use the Highest Quality consensus.

Bases in the consensus sequence can also be edited which will update every sequence at the corresponding position to match what is set in the consensus.

You can also manually move a read mapped to a reference sequence to a specific position in the contig. To do this, select the read and right-click, then choose Move read to position.., and enter the position where you want the left-most base in the read to sit.


PIC


Figure 10.7: Highlight disagreements and edit to resolve them